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- PDB-6oib: Crystal structure of human Sulfide Quinone Oxidoreductase in comp... -

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Basic information

Entry
Database: PDB / ID: 6oib
TitleCrystal structure of human Sulfide Quinone Oxidoreductase in complex with coenzyme Q
ComponentsSulfide:quinone oxidoreductase, mitochondrial
KeywordsOXIDOREDUCTASE
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 / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / HYDROSULFURIC ACID / UBIQUINONE-1 / Sulfide:quinone oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsBanerjee, R. / Cho, U.S. / Kim, H. / Moon, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM130183 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK111465 United States
CitationJournal: Cell Chem Biol / Year: 2019
Title: A Catalytic Trisulfide in Human Sulfide Quinone Oxidoreductase Catalyzes Coenzyme A Persulfide Synthesis and Inhibits Butyrate Oxidation.
Authors: Landry, A.P. / Moon, S. / Kim, H. / Yadav, P.K. / Guha, A. / Cho, U.S. / Banerjee, R.
History
DepositionApr 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,49812
Polymers93,9482
Non-polymers2,55010
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Homo-dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-49 kcal/mol
Surface area30350 Å2
2
A: Sulfide:quinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4207
Polymers46,9741
Non-polymers1,4466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Sulfide:quinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0785
Polymers46,9741
Non-polymers1,1044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.516, 111.512, 133.648
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 46973.863 Da / Num. of mol.: 2 / Fragment: residues 42-450
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SQOR, SQRDL, CGI-44 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y6N5, Oxidoreductases; Acting on a sulfur group of donors; With a quinone or similar compound as acceptor

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Non-polymers , 5 types, 200 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-UQ1 / UBIQUINONE-1


Mass: 250.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H18O4
#5: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M ammonium tartrate dibasic, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 2.03→51.46 Å / Num. obs: 73848 / % possible obs: 96.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.079 / Net I/σ(I): 6
Reflection shellResolution: 2.03→2.08 Å / Rmerge(I) obs: 1.664 / Num. unique obs: 4449 / Rpim(I) all: 0.798

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→41.37 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 3815 2.71 %0.1
Rwork0.2089 ---
obs0.2099 73709 96.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6410 0 170 190 6770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086743
X-RAY DIFFRACTIONf_angle_d0.99149
X-RAY DIFFRACTIONf_dihedral_angle_d11.9113987
X-RAY DIFFRACTIONf_chiral_restr0.055988
X-RAY DIFFRACTIONf_plane_restr0.0061147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.05570.3941090.37933878X-RAY DIFFRACTION74
2.0557-2.08280.41071230.37144359X-RAY DIFFRACTION83
2.0828-2.11130.38231360.34734905X-RAY DIFFRACTION92
2.1113-2.14140.38021380.31555018X-RAY DIFFRACTION95
2.1414-2.17340.33291470.29285152X-RAY DIFFRACTION97
2.1734-2.20740.2891440.28265154X-RAY DIFFRACTION98
2.2074-2.24360.31151440.28295212X-RAY DIFFRACTION98
2.2436-2.28220.36261430.29775106X-RAY DIFFRACTION98
2.2822-2.32370.31741480.26055184X-RAY DIFFRACTION98
2.3237-2.36840.29251470.24965192X-RAY DIFFRACTION98
2.3684-2.41680.33111440.24455201X-RAY DIFFRACTION98
2.4168-2.46930.28981470.23835173X-RAY DIFFRACTION99
2.4693-2.52670.27471440.22735240X-RAY DIFFRACTION99
2.5267-2.58990.23751470.22375151X-RAY DIFFRACTION99
2.5899-2.65990.26161400.2115248X-RAY DIFFRACTION99
2.6599-2.73820.28171430.21565191X-RAY DIFFRACTION99
2.7382-2.82650.28171470.21155199X-RAY DIFFRACTION98
2.8265-2.92750.25631300.21354700X-RAY DIFFRACTION88
2.9275-3.04470.26171420.20575194X-RAY DIFFRACTION98
3.0447-3.18320.27271460.2085258X-RAY DIFFRACTION99
3.1832-3.3510.22821450.19655241X-RAY DIFFRACTION100
3.351-3.56090.18741440.19245254X-RAY DIFFRACTION99
3.5609-3.83560.23481470.18365225X-RAY DIFFRACTION99
3.8356-4.22130.24141480.16765247X-RAY DIFFRACTION99
4.2213-4.83130.17041440.15635254X-RAY DIFFRACTION99
4.8313-6.08380.18821370.16014838X-RAY DIFFRACTION92
6.0838-41.37870.19761410.18395215X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°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)
10.94010.2437-0.24081.6498-0.22211.6536-0.04730.0755-0.1185-0.07030.0322-0.17540.04620.10570.0160.1468-0.0231-0.00750.192-0.02790.229715.962627.282-24.0967
21.2537-0.56350.48691.5727-0.24421.1736-0.0749-0.03260.22320.16730.0196-0.2062-0.16960.03190.04260.21540.0038-0.05290.1792-0.00760.232819.032559.8632-10.68
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 41 through 447)
2X-RAY DIFFRACTION2(chain 'B' and resid 41 through 446)

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