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- PDB-6mo6: Crystal structure of the selenomethionine-substituted human sulfi... -

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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
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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