[English] 日本語
Yorodumi
- PDB-6mo6: Crystal structure of the selenomethionine-substituted human sulfi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mo6
TitleCrystal structure of the selenomethionine-substituted human sulfide:quinone oxidoreductase
ComponentsSulfide:quinone oxidoreductase, mitochondrial
Keywordsmembrane protein / oxidoreductase / sulfide:quinone oxidoreductase / Rossman fold / hydrogen sulfide metabolism / thiocystine
Function / homology
Function and homology information


eukaryotic sulfide quinone oxidoreductase / glutathione-dependent sulfide quinone oxidoreductase activity / sulfide oxidation, using sulfide:quinone oxidoreductase / Sulfide oxidation to sulfate / sulfide:quinone oxidoreductase activity / quinone binding / FAD binding / mitochondrial inner membrane / mitochondrion
Similarity search - Function
Sulphide quinone-reductase / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Sulfide:quinone oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å
AuthorsJackson, M.R. / Jorns, M.S. / Loll, P.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM107389 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R41 HL134435 United States
CitationJournal: Structure / Year: 2019
Title: X-Ray Structure of Human Sulfide:Quinone Oxidoreductase: Insights into the Mechanism of Mitochondrial Hydrogen Sulfide Oxidation.
Authors: Jackson, M.R. / Loll, P.J. / Jorns, M.S.
History
DepositionOct 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfide:quinone oxidoreductase, mitochondrial
B: Sulfide:quinone oxidoreductase, mitochondrial
C: Sulfide:quinone oxidoreductase, mitochondrial
D: Sulfide:quinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,53612
Polymers188,2524
Non-polymers3,2848
Water4,990277
1
A: Sulfide:quinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8843
Polymers47,0631
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sulfide:quinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8843
Polymers47,0631
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sulfide:quinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8843
Polymers47,0631
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sulfide:quinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8843
Polymers47,0631
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.390, 119.390, 551.858
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

-
Components

#1: Protein
Sulfide:quinone oxidoreductase, mitochondrial / SQOR / Sulfide dehydrogenase-like / Sulfide quinone oxidoreductase


Mass: 47062.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SQOR, SQRDL, CGI-44 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9Y6N5, Oxidoreductases; Acting on a sulfur group of donors; With a quinone or similar compound as acceptor
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.79 %
Description: bright yellow obelisk-shaped crystals with typical linear dimensions of 0.08 x 0.08 x 0.5 cubic mm
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 500 uL reservoir of 20% (w/v) glycerol, 0.1 M sodium acetate trihydrate pH 4.6, 0.3-0.5 M ammonium acetate, 7-10% (w/v) PEG 4,000, 0.1% (w/v) 1,2-diheptanoyl-sn-glycero-3-phosphocholine ...Details: 500 uL reservoir of 20% (w/v) glycerol, 0.1 M sodium acetate trihydrate pH 4.6, 0.3-0.5 M ammonium acetate, 7-10% (w/v) PEG 4,000, 0.1% (w/v) 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC), 310 uM decylubiquinone (DCQ; stock in 10% (w/v) DHPC) and 10 mM sodium thiosulfate pentahydrate. To the coverslip; apply 1 uL aliquot of 10.66% (w/v) 1-Oleoyl-rac-glycerol (monoolein; stock in ethanol) and air dry for 3 minutes. Add 1uL enzyme followed by 1uL reservoir condition (no mixing).
Temp details: daily fluctuation as low as 288K to 302K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.59→68.72 Å / Num. obs: 68911 / % possible obs: 93.7 % / Redundancy: 85.7 % / Biso Wilson estimate: 40.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.027 / Rrim(I) all: 0.253 / Net I/σ(I): 22.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.59-2.6581.81.65527760.6460.181.66660.5
12.42-68.7273.40.0678380.9990.0080.06899.5

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
REFMAC5.8.0222refinement
MOSFLM7.2.0data reduction
Aimless0.6.3data scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.59→62.692 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.11
RfactorNum. reflection% reflection
Rfree0.2449 3406 4.94 %
Rwork0.1869 --
obs0.1897 68902 93.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 151.83 Å2 / Biso mean: 39.568 Å2 / Biso min: 17.75 Å2
Refinement stepCycle: final / Resolution: 2.59→62.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13040 0 216 277 13533
Biso mean--33.93 35.78 -
Num. residues----1654
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.59-2.6270.2909940.2281649174359
2.627-2.66620.3087910.21581838192964
2.6662-2.70790.2487970.20982084218172
2.7079-2.75230.30691210.21352406252784
2.7523-2.79970.28651330.21182694282794
2.7997-2.85060.2471660.21232747291396
2.8506-2.90550.29151470.21892795294298
2.9055-2.96480.30941590.23972797295698
2.9648-3.02920.32221490.22712810295998
3.0292-3.09970.30611530.21512835298898
3.0997-3.17720.29791440.20422845298998
3.1772-3.26310.27641420.19872848299098
3.2631-3.35910.25541630.20342843300698
3.3591-3.46760.25591480.20282863301199
3.4676-3.59150.26141430.20352781292496
3.5915-3.73530.23481490.1892878302799
3.7353-3.90520.25631600.17082868302899
3.9052-4.11110.17411580.15722907306599
4.1111-4.36860.19721330.15332910304399
4.3686-4.70580.19061560.14922937309399
4.7058-5.17920.21181600.15452951311198
5.1792-5.92810.21981120.17252930304297
5.9281-7.46680.21451500.17963072322299
7.4668-62.71020.26681780.20363208338698

+
About Yorodumi

-
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://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

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 homology information / Changes in new EM Navigator and Yorodumi

Read more