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- PDB-6mp5: Crystal structure of native human sulfide:quinone oxidoreductase -

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Basic information

Entry
Database: PDB / ID: 6mp5
TitleCrystal structure of native 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.99 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
Citation
Journal: 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.
#1: Journal: Meth. Enzymol. / Year: 2015
Title: Role of human sulfide: quinone oxidoreductase in H2S metabolism.
Authors: Jackson, M.R. / Melideo, S.L. / Jorns, M.S.
#2: Journal: Biochemistry / Year: 2012
Title: Human sulfide:quinone oxidoreductase catalyzes the first step in hydrogen sulfide metabolism and produces a sulfane sulfur metabolite.
Authors: Jackson, M.R. / Melideo, S.L. / Jorns, M.S.
History
DepositionOct 5, 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 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Sulfide:quinone oxidoreductase, mitochondrial
D: Sulfide:quinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,4038
Polymers185,2614
Non-polymers3,1424
Water50428
1
A: Sulfide:quinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1012
Polymers46,3151
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sulfide:quinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1012
Polymers46,3151
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sulfide:quinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1012
Polymers46,3151
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sulfide:quinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1012
Polymers46,3151
Non-polymers7861
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

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Components

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


Mass: 46315.207 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: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.07 Å3/Da / Density % sol: 59.91 % / Description: bright yellow hexagonal rods
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 14% (w/v) PEG 4000, 10% (w/v) glycerol, 0.1M sodium acetate trihydrate pH 4.6, 0.5M ammonium acetate + 0.1% (w/v) 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC). Apply 1uL protein then ...Details: 14% (w/v) PEG 4000, 10% (w/v) glycerol, 0.1M sodium acetate trihydrate pH 4.6, 0.5M ammonium acetate + 0.1% (w/v) 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC). Apply 1uL protein then 1uL condition (no mixing) to coverslip and seal.
Temp details: daily fluctuation from 288K low to 302K high

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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: Jul 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.99→96.79 Å / Num. obs: 48607 / % possible obs: 100 % / Redundancy: 15.8 % / Biso Wilson estimate: 72.01 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.326 / Rpim(I) all: 0.083 / Rrim(I) all: 0.336 / Net I/σ(I): 9.6 / Num. measured all: 770154 / Scaling rejects: 2173
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.99-3.0911.62.7595022343150.2240.8322.8881.199.9
11.96-96.7911.90.042113389530.9990.0130.04426.699.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.72 Å96.79 Å
Translation4.72 Å96.79 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
Aimless0.6.3data scaling
PHASER2.8.2phasing
DMphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MO6

6mo6


Resolution: 2.99→90.133 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.48
RfactorNum. reflection% reflection
Rfree0.2642 2377 4.91 %
Rwork0.2082 --
obs0.2109 48446 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.79 Å2 / Biso mean: 69.2723 Å2 / Biso min: 38.21 Å2
Refinement stepCycle: final / Resolution: 2.99→90.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13020 0 212 28 13260
Biso mean--61.16 54.18 -
Num. residues----1652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413568
X-RAY DIFFRACTIONf_angle_d0.62418408
X-RAY DIFFRACTIONf_chiral_restr0.0462004
X-RAY DIFFRACTIONf_plane_restr0.0052316
X-RAY DIFFRACTIONf_dihedral_angle_d4.4598060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.99-3.05110.41851370.3532575271299
3.0511-3.11740.39191380.33126382776100
3.1174-3.18990.3711330.304626512784100
3.1899-3.26970.34541310.281126382769100
3.2697-3.35810.31881530.258126622815100
3.3581-3.45690.29781470.263126352782100
3.4569-3.56850.33811250.230526922817100
3.5685-3.69610.25671330.237326902823100
3.6961-3.8440.26331570.210426672824100
3.844-4.0190.29481410.210426602801100
4.019-4.23090.21871370.177327002837100
4.2309-4.49590.22731260.163427322858100
4.4959-4.84310.21231530.164327022855100
4.8431-5.33040.24541350.168327552890100
5.3304-6.10160.21681140.177428112925100
6.1016-7.68670.21561470.195528342981100
7.6867-90.17370.26681700.202230273197100

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