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- PDB-3h8i: The first X-ray structure of a sulfide:quinone oxidoreductase: In... -

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Basic information

Entry
Database: PDB / ID: 3h8i
TitleThe first X-ray structure of a sulfide:quinone oxidoreductase: Insights into sulfide oxidation mechanism
ComponentsNADH oxidase
KeywordsOXIDOREDUCTASE / Membrane protein / rossman-like fold
Function / homology
Function and homology information


bacterial sulfide:quinone reductase / sulfide:quinone oxidoreductase activity / quinone binding / nucleotide binding / membrane
Similarity search - Function
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 / PHOSPHATE ION / trisulfane / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAcidianus ambivalens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.65 Å
AuthorsBrito, J.A. / Sousa, F.L. / Stelter, M. / Bandeiras, T.M. / Vonrhein, C. / Teixeira, M. / Pereira, M.M. / Archer, M.
CitationJournal: Biochemistry / Year: 2009
Title: Structural and functional insights into sulfide:quinone oxidoreductase.
Authors: Brito, J.A. / Sousa, F.L. / Stelter, M. / Bandeiras, T.M. / Vonrhein, C. / Teixeira, M. / Pereira, M.M. / Archer, M.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH oxidase
B: NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,97115
Polymers90,3492
Non-polymers2,62213
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-86 kcal/mol
Surface area29140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.550, 178.550, 162.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein NADH oxidase


Mass: 45174.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acidianus ambivalens (archaea) / References: UniProt: Q7ZAG8, NADH dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-S3H / trisulfane


Mass: 98.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO THE AUTHORS THE UNP DATABASE SEQUENCE IS IN ERROR AT THIS POSITION

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.1370.24
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop8.52.2 M NH4H2PO4, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop4.52.2 M NH4H2PO4/K2HPO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.65→47.43 Å / Num. obs: 44293 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 71.62 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.2
Reflection shellResolution: 2.65→2.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2 / Num. unique all: 6392 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
SHARPphasing
BUSTER-TNT2.7.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.65→26.66 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 2235 5.05 %RANDOM
Rwork0.1955 ---
obs0.197 44225 98.96 %-
Displacement parametersBiso mean: 56.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.4377 Å20 Å20 Å2
2---0.4377 Å20 Å2
3---0.8754 Å2
Refinement stepCycle: LAST / Resolution: 2.65→26.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5588 0 157 171 5916
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00658872
X-RAY DIFFRACTIONt_angle_deg0.90779772
X-RAY DIFFRACTIONt_dihedral_angle_d16.2411962
X-RAY DIFFRACTIONt_trig_c_planes0.0061602
X-RAY DIFFRACTIONt_gen_planes0.0128795
X-RAY DIFFRACTIONt_it0.914588720
X-RAY DIFFRACTIONt_nbd0925
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3087 140 4.62 %
Rwork0.2371 2892 -
all0.2404 3032 -
obs--98.96 %

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