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- PDB-3hyv: 3-D X-Ray structure of the sulfide:quinone oxidoreductase from th... -

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Basic information

Entry
Database: PDB / ID: 3hyv
Title3-D X-Ray structure of the sulfide:quinone oxidoreductase from the hyperthermophilic bacterium Aquifex aeolicus
ComponentsSulfide-quinone reductaseSulfide:quinone reductase
KeywordsOXIDOREDUCTASE / PROTEIN COMPLEX / MONOTOPIC MEMBRANE PROTEIN / FLAVOPROTEIN / ROSSMANN-FOLD DOMAIN
Function / homology
Function and homology information


bacterial sulfide:quinone reductase / sulfide:quinone oxidoreductase activity / aerobic electron transport chain / NAD(P)H dehydrogenase (quinone) activity / quinone binding / nucleotide binding / membrane / identical protein binding
Similarity search - Function
FAD/NAD(P)-binding domain - #100 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / 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 / octathiocane / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsMarcia, M. / Ermler, U. / Peng, G.H. / Michel, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration
Authors: Marcia, M. / Ermler, U. / Peng, G.H. / Michel, H.
History
DepositionJun 23, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionJul 14, 2009ID: 3H27
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfide-quinone reductase
B: Sulfide-quinone reductase
C: Sulfide-quinone reductase
D: Sulfide-quinone reductase
E: Sulfide-quinone reductase
F: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,46461
Polymers285,2106
Non-polymers13,25455
Water10,287571
1
A: Sulfide-quinone reductase
C: Sulfide-quinone reductase
E: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,20031
Polymers142,6053
Non-polymers6,59528
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Sulfide-quinone reductase
D: Sulfide-quinone reductase
F: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,26430
Polymers142,6053
Non-polymers6,65927
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Sulfide-quinone reductase
B: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,49821
Polymers95,0702
Non-polymers4,42919
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-174 kcal/mol
Surface area33620 Å2
MethodPISA
4
E: Sulfide-quinone reductase
F: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,40220
Polymers95,0702
Non-polymers4,33318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-175 kcal/mol
Surface area33800 Å2
MethodPISA
5
C: Sulfide-quinone reductase
D: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,56320
Polymers95,0702
Non-polymers4,49318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-172 kcal/mol
Surface area33840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.850, 154.920, 178.040
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 / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein
Sulfide-quinone reductase / Sulfide:quinone reductase / sulfide:quinone oxidoreductase


Mass: 47534.918 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Aquifex aeolicus (bacteria) / Strain: VF5
References: UniProt: O67931, Oxidoreductases; Acting on a sulfur group of donors; With a quinone or similar compound as acceptor
#3: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 6 types, 620 molecules

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


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H2S
#5: Chemical
ChemComp-PS9 / octathiocane / Octasulfur


Mass: 256.520 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: S8
#6: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE SIDE CHAIN OF CYS156 IS EXTENDED TO FORM A PUTATIVE POLYSULFUR CHAIN. ONE SULFUR ATOM OF THE ...THE SIDE CHAIN OF CYS156 IS EXTENDED TO FORM A PUTATIVE POLYSULFUR CHAIN. ONE SULFUR ATOM OF THE CHAIN IS DESCRIBED AS LINKED TO THE CYS AND FORM A S-MERCAPTO-CYSTEINE, CSS. THE REST OF THE CHAIN TAKES THE FORM OF A CYCLOOCTASULFUR SPECIES PS9 IN SEVERAL MONOMERS AND MIGHT REPRESENT THE PRODUCT OF THE REACTION CATALYZED BY THE PROTEIN. H2S INDICATES A PUTATIVE S ATOM BRIDGING CYS124 AND FAD. THIS S ATOM IS POSSIBLY CONTRIBUTED BY THE SUBSTRATE OF THE PROTEIN, HYDROGEN SULFIDE. PLEASE REFER TO THE RELATED PUBLICATION FOR A MORE DETAILED DESCRIPTION OF THE PUTATIVE SULFUR LIGANDS OF THE SULFIDE:QUINONE OXIDOREDUCTASE.

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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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 4% PEG 400 (V/V), 0.1M NA-MES (SODIUM 2-(N-MORPHOLINO)-ETHANESULFONATE), 2M AMMONIUM SULFATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.91984
SYNCHROTRONSLS X06SA21.14000, 1.14050, 1.13010, 1.03864
Detector
TypeIDDetectorDateDetails
MARMOSAIC 225 mm CCD1CCDFeb 24, 2008dynamically bendable mirror
PSI PILATUS 6M2PIXELFeb 24, 2008dynamically bendable mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LN2 cooled fixed-exit Si(111) monochromator, sagittalSINGLE WAVELENGTHMx-ray1
2LN2 cooled fixed-exit Si(111) monochromator, sagittalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.919841
21.141
31.14051
41.13011
51.038641
ReflectionResolution: 2.3→50 Å / Num. obs: 135807 / % possible obs: 97.9 % / Redundancy: 3.47 % / Net I/σ(I): 14.87
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.47 % / Mean I/σ(I) obs: 3.44 / % possible all: 87.9

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Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→20.04 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.13 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23537 6821 5 %RANDOM
Rwork0.19321 ---
obs0.19534 128783 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.517 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å20 Å2
2---0.09 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20016 0 768 571 21355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02221516
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2542.00529260
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.35152602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21724.364873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77153420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0521584
X-RAY DIFFRACTIONr_chiral_restr0.080.23186
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216028
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.28194
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.214253
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2741
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4121.513414
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.648221012
X-RAY DIFFRACTIONr_scbond_it1.04339748
X-RAY DIFFRACTIONr_scangle_it1.6544.58231
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 444 -
Rwork0.226 8051 -
obs--84.89 %

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