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- PDB-8dhk: Crystal structure of human Sulfide Quinone Oxidoreductase K207E -

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Basic information

Entry
Database: PDB / ID: 8dhk
TitleCrystal structure of human Sulfide Quinone Oxidoreductase K207E
ComponentsSulfide:quinone oxidoreductase
KeywordsOXIDOREDUCTASE / K207E / FAD / Sulfide:quinone oxidoreductase / mitochondrial / trisulfide
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 / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / DI(HYDROXYETHYL)ETHER / Sulfide:quinone oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMascarenhas, R.N. / Ludlum, A. / Banerjee, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM130183 United States
CitationJournal: To Be Published
Title: Sulfide oxidation in human sulfide quinone oxidoreductase is enthalpically driven: Contributions of the Lys-207 general base
Authors: Bonanata, J. / Landry, A. / Ceric, K. / Ludlam, A. / Mascarenhas, R. / Coitino, L. / Banerjee, R.
History
DepositionJun 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,51521
Polymers94,0122
Non-polymers3,50319
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-45 kcal/mol
Surface area30260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.793, 111.298, 134.105
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Sulfide dehydrogenase-like / Sulfide quinone oxidoreductase


Mass: 47005.863 Da / Num. of mol.: 2 / Mutation: K207E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6N5

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Non-polymers , 5 types, 226 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID


Mass: 190.154 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N2O5 / Comment: pH buffer*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M ADA pH 7, 34% PEG 400 and 0.3 M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→45.1 Å / Num. obs: 51811 / % possible obs: 99.9 % / Redundancy: 8.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.154 / Net I/σ(I): 8
Reflection shellResolution: 2.3→2.37 Å / Rmerge(I) obs: 1.404 / Num. unique obs: 4434 / CC1/2: 0.55

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OI6

6oi6


Resolution: 2.3→33.405 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 2661 5.15 %
Rwork0.1966 49000 -
obs0.1987 51661 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.27 Å2 / Biso mean: 52.6448 Å2 / Biso min: 27.24 Å2
Refinement stepCycle: final / Resolution: 2.3→33.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6315 0 417 207 6939
Biso mean--63.8 47.58 -
Num. residues----811
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.34180.31951570.26722524100
2.3418-2.38690.35991400.27072518100
2.3869-2.43560.30261390.26242541100
2.4356-2.48850.28551120.24952587100
2.4885-2.54640.29651300.23192548100
2.5464-2.610.27851420.22112551100
2.61-2.68060.25941330.21672555100
2.6806-2.75940.29931500.21742552100
2.7594-2.84840.30951360.22892563100
2.8484-2.95020.29421520.21912542100
2.9502-3.06820.29951390.23322572100
3.0682-3.20780.23771230.21142572100
3.2078-3.37670.30041410.21182582100
3.3767-3.58810.23761500.192569100
3.5881-3.86470.2041390.17742622100
3.8647-4.25290.18151410.15722589100
4.2529-4.86670.1791470.15292608100
4.8667-6.12540.20391340.16952666100
6.1254-33.4050.2211560.2106273999

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