PDB-6yyv: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... (2024)

ID or keywords:

Entry

Database: PDB / ID: 6yyv

Title

Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese and 3-methyl-2-oxoglutarate

Components

Aspartyl/asparaginyl beta-hydroxylase

Keywords

OXIDOREDUCTASE / Aspartyl/asparaginyl beta-hydroxylase / Dioxygenase

Function / hom*ology

Function and hom*ology information

peptide-aspartate beta-dioxygenase / regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / regulation of protein depolymerization / activation of store-operated calcium channel activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / peptidyl-aspartic acid 3-dioxygenase activity / sarcoplasmic reticulum lumen / limb morphogenesis / cortical endoplasmic reticulum ...peptide-aspartate beta-dioxygenase / regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / regulation of protein depolymerization / activation of store-operated calcium channel activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / peptidyl-aspartic acid 3-dioxygenase activity / sarcoplasmic reticulum lumen / limb morphogenesis / cortical endoplasmic reticulum / pattern specification process / positive regulation of intracellular protein transport / activation of cysteine-type endopeptidase activity / face morphogenesis / structural constituent of muscle / response to ATP / positive regulation of calcium ion transport into cytosol / roof of mouth development / positive regulation of ryanodine-sensitive calcium-release channel activity / Protein hydroxylation / positive regulation of proteolysis / detection of calcium ion / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / calcium channel complex / muscle contraction / cellular response to calcium ion / calcium ion transmembrane transport / regulation of protein stability / Stimuli-sensing channels / transmembrane transporter binding / cell population proliferation / electron transfer activity / negative regulation of cell population proliferation / calcium ion binding / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / endoplasmic reticulum / plasma membrane
Similarity search - Function

Aspartyl beta-hydroxylase/Triadin domain / Aspartyl/asparaginyl beta-hydroxylase family / Aspartyl beta-hydroxylase N-terminal region / Aspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / Isopenicillin N synthase-like superfamily / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...Aspartyl beta-hydroxylase/Triadin domain / Aspartyl/asparaginyl beta-hydroxylase family / Aspartyl beta-hydroxylase N-terminal region / Aspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / Isopenicillin N synthase-like superfamily / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/hom*ology

: / Chem-Q1Z / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component

Biological species

PDB-6yyv: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... (5)

hom*o sapiens (human)

Method

PDB-6yyv: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... (6)

X-RAY DIFFRACTION /

PDB-6yyv: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... (7)

SYNCHROTRON /

PDB-6yyv: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... (8)

MOLECULAR REPLACEMENT / Resolution: 1.77 Å

PDB-6yyv: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... (9)

Authors

Nakashima, Y. / Brewitz, L. / Schofield, C.J.

PDB-6yyv: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... (10)

Citation

Journal: Chem Sci / Year: 2020
Title: Synthesis of 2-oxoglutarate derivatives and their evaluation as cosubstrates and inhibitors of human aspartate/asparagine-beta-hydroxylase.
Authors: Brewitz, L. / Nakashima, Y. / Schofield, C.J.

History

Deposition	May 6, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 17, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jul 19, 2023	Group: Advisory / Data collection / Database references Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_unobs_or_zero_occ_atoms Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model Item: _diffrn_source.pdbx_synchrotron_site

Structure viewer	Molecule: MolmilJmol/JSmol

PDB-6yyv: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... (14)

Download

PDBx/mmCIF format	6yyv.cif.gz	324.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6yyv.ent.gz	219.6 KB	Display	PDB format
PDBx/mmJSON format	6yyv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

Validation report

Summary document	6yyv_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6yyv_full_validation.pdf.gz	1.2 MB	Display
Data in XML	6yyv_validation.xml.gz	22.2 KB	Display
Data in CIF	6yyv_validation.cif.gz	33.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yy/6yyv ftp://data.pdbj.org/pub/pdb/validation_reports/yy/6yyv	HTTPS FTP

Related structure data

Related structure data	6yyuC 6yywC 6yyyC 6z6qC 6z6rC 5jzaS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6qa5-d 6yyu-d 6yyw-d 6yyx-d 6yyy-d 5jqy-d 6z6q-d 6z6r-d 5zkb-d 5jzu-d Search similar-shape structures by Omokage search (details) F&H Search Similarity search - FunctionF&H Search Similarity search - hom*ologyF&H Search

PDB-6yyv: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... (53)

Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#141 - Sep 2011 O-GlcNAc Transferase similarity (4) #230 - Feb 2019 Initiation Factor eIF4E similarity (4) #166 - Oct 2013 Proteasome similarity (3) #44 - Aug 2003 Calmodulin similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1)

Deposited unit

A: Aspartyl/asparaginyl beta-hydroxylase

hetero molecules

49.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

	Theoretical mass	Number of molelcules
Total (without water)	49,620	3
Polymers	49,405	1
Non-polymers	215	2
Water	7,350	408

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Buried area	130 Å²
ΔG^int	-7 kcal/mol
Surface area	19950 Å²
Method	PISA

Unit cell

Length a, b, c (Å)	48.802, 70.521, 174.488
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Aspartyl/asparaginyl beta-hydroxylase / Aspartate beta-hydroxylase / ASP beta-hydroxylase / Peptide-aspartate beta-dioxygenase Mass: 49405.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) homo sapiens* (human) / Gene: ASPH, BAH / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q12797, peptide-aspartate beta-dioxygenase
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-Q1Z / (3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid Mass: 160.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₅ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

PDB-6yyv: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... (85)

Sample preparation

Crystal	Density Matthews: 3.04 Å³/Da / Density % sol: 59.49 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9 Details: 200 mM magnesium acetate tetrahydrate, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM 3-methyl-2-oxoglutarate, 18 mg/ml protein

Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 1, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97623 Å / Relative weight: 1
Reflection	Resolution: 1.77→87.24 Å / Num. obs: 43399 / % possible obs: 94.2 % / Redundancy: 13.3 % / B_iso Wilson estimate: 32.09 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.11 / Net I/σ(I): 16.1
Reflection shell	Resolution: 1.77→1.96 Å / R_merge(I) obs: 1.876 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2170 / CC_1/2: 0.54

PDB-6yyv: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... (89)

Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

PDB-6yyv: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... (90)

MOLECULAR REPLACEMENT
Starting model: 5JZA

5jza

Resolution: 1.77→43.62 Å / SU ML: 0.1687 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5691

	R_factor	Num. reflection	% reflection
R_free	0.2084	2111	4.86 %
R_work	0.1727	-	-
obs	0.1745	43399	72.75 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 52.66 Å²

Refinement step

Cycle: LAST / Resolution: 1.77→43.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3392	0	11	408	3811

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0119	3511
X-RAY DIFFRACTION	f_angle_d	1.1495	4759
X-RAY DIFFRACTION	f_chiral_restr	0.0579	503
X-RAY DIFFRACTION	f_plane_restr	0.0087	625
X-RAY DIFFRACTION	f_dihedral_angle_d	21.7195	1307

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.77-1.81	0.3435	6	0.2732	85	X-RAY DIFFRACTION	2.33
1.81-1.86	0.2853	8	0.2735	175	X-RAY DIFFRACTION	4.77
1.86-1.91	0.2051	23	0.2722	523	X-RAY DIFFRACTION	13.94
1.91-1.96	0.3512	63	0.2664	1323	X-RAY DIFFRACTION	35.42
1.96-2.03	0.2506	114	0.2392	2050	X-RAY DIFFRACTION	55.13
2.03-2.1	0.2871	144	0.2302	2818	X-RAY DIFFRACTION	75.75
2.1-2.18	0.2635	190	0.2133	3709	X-RAY DIFFRACTION	98.93
2.18-2.28	0.2273	191	0.1995	3743	X-RAY DIFFRACTION	99.9
2.28-2.4	0.2346	184	0.1879	3770	X-RAY DIFFRACTION	99.97
2.4-2.55	0.2026	171	0.1793	3801	X-RAY DIFFRACTION	100
2.55-2.75	0.2162	214	0.1913	3759	X-RAY DIFFRACTION	99.97
2.75-3.03	0.2299	196	0.1864	3810	X-RAY DIFFRACTION	99.98
3.03-3.47	0.2567	172	0.1745	3837	X-RAY DIFFRACTION	100
3.47-4.36	0.1714	206	0.1384	3862	X-RAY DIFFRACTION	100
4.37-43.62	0.1799	229	0.1577	4023	X-RAY DIFFRACTION	99.86

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.80413604063	0.679471214675	1.48657199705	4.21105761513	0.549702327149	1.5046568519	0.222004802293	1.14644767976	-0.0731030708531	-1.71114899059	-0.0148749498426	-1.07365656444	0.240142126711	0.626140899661	-0.432882622156	1.57138123515	0.325655506276	0.463818585998	1.41498573795	-0.293898698776	0.796670549456	-13.5944834734	8.83377957262	-72.8512310656
2	1.205577616	-0.420640375367	0.316460771984	2.01750401565	-1.11056264216	1.24470067746	0.13979677591	0.247877366602	0.0438636827668	-0.52814750535	-0.14546543448	-0.205741286381	0.25185953907	-0.00472344585544	-0.0197389516245	0.432851495718	0.0411592434152	0.00931535930049	0.129500221228	-0.0445573420258	0.256625175928	-24.4962606048	7.24863062573	-49.4543052326
3	1.88319810954	0.414238495074	0.663144245192	0.884661264897	0.576269379042	1.33600847286	0.0148520309196	-0.059114127672	-0.226848988222	-0.104978321345	0.13473410578	-0.114739895335	0.147091843276	0.194371606902	-0.101659282276	0.234033259623	0.0242731056476	0.000554555048719	0.20108297142	-0.0724139037719	0.235680572663	-6.90916852218	-0.343930493646	-24.2584906448
4	2.3552677238	0.191440116104	0.220542968548	1.00171419823	0.622484753401	0.992427891204	0.00890890401374	-0.35852392834	0.274333898173	-0.151916501014	0.027209279492	-0.0406667375325	-0.118559251769	0.0257353856575	-0.0527241494638	0.159700444216	0.0104178211379	-0.00311462397666	0.25662160567	-0.0847566569908	0.203314828912	-6.00490510982	13.4002513382	-13.1719682759

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 330 through 374 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 375 through 517 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 518 through 593 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 594 through 758 )

News

Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology

In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.

Severe acute respiratory syndrome coronavirus 2 | Severe acute respiratory syndrome coronavirus 2
SARS-CoV-2 - Yorodumi Search

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

Jul 12, 2017. Major update of PDB

Major update of PDB

wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and hom*ology information / Changes in new EM Navigator and Yorodumi