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- PDB-6oi6: Crystal structure of human Sulfide Quinone Oxidoreductase in comp... -

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Basic information

Entry
Database: PDB / ID: 6oi6
TitleCrystal structure of human Sulfide Quinone Oxidoreductase in complex with coenzyme Q (sulfide soaked)
ComponentsSulfide:quinone oxidoreductase, mitochondrialSulfide:quinone reductase
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 superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / UBIQUINONE-1 / Sulfide:quinone oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 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 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release

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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)96,0846
Polymers94,0122
Non-polymers2,0724
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Homo-dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-26 kcal/mol
Surface area31360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.532, 111.959, 136.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 47005.930 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
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


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


Mass: 250.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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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: 60.48 %
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: 2.55→50.98 Å / Num. all: 205379 / Num. obs: 38478 / % possible obs: 99.24 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.095 / Rrim(I) all: 0.223 / Net I/σ(I): 4.5
Reflection shellResolution: 2.55→2.6 Å / Rmerge(I) obs: 1.139 / Num. unique obs: 1642 / Rpim(I) all: 0.522

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→50.934 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 29.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 3773 5.21 %
Rwork0.2053 --
obs0.2084 72432 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→50.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6394 0 142 38 6574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096701
X-RAY DIFFRACTIONf_angle_d0.9969096
X-RAY DIFFRACTIONf_dihedral_angle_d16.7773968
X-RAY DIFFRACTIONf_chiral_restr0.056986
X-RAY DIFFRACTIONf_plane_restr0.0071142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.59240.34321380.29282528X-RAY DIFFRACTION100
2.5924-2.62650.36451430.29192557X-RAY DIFFRACTION100
2.6265-2.66250.3741440.28742567X-RAY DIFFRACTION100
2.6625-2.70050.34581360.29432526X-RAY DIFFRACTION100
2.7005-2.74080.30711410.28182571X-RAY DIFFRACTION99
2.7408-2.78370.38131360.27962540X-RAY DIFFRACTION99
2.7837-2.82930.3721400.27212545X-RAY DIFFRACTION99
2.8293-2.87810.32351390.27352527X-RAY DIFFRACTION99
2.8781-2.93040.33811380.25982495X-RAY DIFFRACTION98
2.9304-2.98680.34791350.25562504X-RAY DIFFRACTION99
2.9868-3.04770.33651440.25392593X-RAY DIFFRACTION100
3.0477-3.1140.33251420.25182570X-RAY DIFFRACTION100
3.114-3.18640.30981430.2472530X-RAY DIFFRACTION100
3.1864-3.26610.3061420.23762574X-RAY DIFFRACTION100
3.2661-3.35440.34571410.22872510X-RAY DIFFRACTION100
3.3544-3.45310.27421390.21492582X-RAY DIFFRACTION100
3.4531-3.56450.33251380.20252551X-RAY DIFFRACTION99
3.5645-3.69190.25021370.17882555X-RAY DIFFRACTION100
3.6919-3.83960.23111400.18612558X-RAY DIFFRACTION100
3.8396-4.01430.20991400.16652574X-RAY DIFFRACTION99
4.0143-4.22580.18531360.16052520X-RAY DIFFRACTION100
4.2258-4.49050.20261380.15612552X-RAY DIFFRACTION100
4.4905-4.83690.21711420.15522516X-RAY DIFFRACTION98
4.8369-5.32320.2391450.15142519X-RAY DIFFRACTION99
5.3232-6.09240.17441370.16152492X-RAY DIFFRACTION98
6.0924-7.67160.23551490.17642567X-RAY DIFFRACTION100
7.6716-50.94430.24191300.21922536X-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)
10.7879-0.1922-0.03341.5397-0.06411.3044-0.0506-0.12930.07430.13170.0426-0.1339-0.04310.08020.0150.18450.024-0.03280.252-0.01950.2544-22.50327.708424.5867
21.34530.3995-0.56361.233-0.09231.5117-0.0993-0.0197-0.2394-0.1840.0048-0.16480.23430.03320.09330.34580.02790.04410.2640.01070.3322-20.2411-4.63149.8089
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 42 through 445)

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