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- PDB-4wqe: Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - K2... -

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Basic information

Entry
Database: PDB / ID: 4wqe
TitleThiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - K208G mutant
ComponentsThiosulfate dehydrogenase
KeywordsOXIDOREDUCTASE / tetrathionate / TsdA / c-type cytochrome
Function / homology
Function and homology information


thiosulfate dehydrogenase / thiosulfate dehydrogenase activity / periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
SoxA/TsdA, cytochrome c domain / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / IODIDE ION / SULFITE ION / THIOSULFATE / Thiosulfate dehydrogenase
Similarity search - Component
Biological speciesAllochromatium vinosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBrito, J.A. / Denkmann, K. / Pereira, I.A.C. / Dahl, C. / Archer, M.
Funding support Portugal, Germany, 7items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/QUI-BIQ/100591/2008 Portugal
Fundacao para a Ciencia e a TecnologiaPTDC/BIA-PRO/118535/2010 Portugal
Fundacao para a Ciencia e a TecnologiaPEst-OE/EQB/LA0004/2011 Portugal
German Academic Exchange Service Germany
Conselho de Reitores das Universidades Portuguesas Portugal
BioStruct-X1493
Fundacao para a Ciencia e a TecnologiaSFRH/BPD/79224/2011 Portugal
Citation
Journal: J.Biol.Chem. / Year: 2015
Title: Thiosulfate Dehydrogenase (TsdA) from Allochromatium vinosum: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO THIOSULFATE OXIDATION.
Authors: Brito, J.A. / Denkmann, K. / Pereira, I.A. / Archer, M. / Dahl, C.
#1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2014
Title: Production, crystallization and preliminary crystallographic analysis of Allochromatium vinosum thiosulfate dehydrogenase TsdA, an unusual acidophilic c-type cytochrome.
Authors: Brito, J.A. / Gutierres, A. / Denkmann, K. / Dahl, C. / Archer, M.
History
DepositionOct 21, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiosulfate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5537
Polymers26,9011
Non-polymers1,6526
Water3,963220
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-56 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.266, 70.656, 57.948
Angle α, β, γ (deg.)90.00, 129.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1123-

HOH

21A-1129-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thiosulfate dehydrogenase / Tetrathionate synthase


Mass: 26901.268 Da / Num. of mol.: 1 / Mutation: K208G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium vinosum (bacteria) / Strain: ATCC 17899 / DSM 180 / NBRC 103801 / D / Gene: tsdA, Alvin_0091 / Plasmid: pPR-IBAAvtsdAs / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3RVD4, thiosulfate dehydrogenase

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Non-polymers , 6 types, 226 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-THJ / THIOSULFATE


Mass: 112.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O3S2
#6: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.28
Details: 23.5% (w/v) PEG 3350, 0.1 M Bis-tris pH 6.28, 0.2 M (NH4)2SO4, 0.1 M NaI

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Data collection

DiffractionMean temperature: 100.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.4→35.33 Å / Num. obs: 82008 / % possible obs: 64 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.55
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.31 / Num. unique all: 1837 / % possible all: 53

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Processing

Software
NameVersionClassification
XDSdata reduction
Coot0.7.1model building
PHENIX(phenix.refine: dev_1830)refinement
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→35.33 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1701 3045 4.95 %
Rwork0.1382 --
obs0.1398 61494 64.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 101 220 2017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121892
X-RAY DIFFRACTIONf_angle_d1.4922595
X-RAY DIFFRACTIONf_dihedral_angle_d16.678679
X-RAY DIFFRACTIONf_chiral_restr0.066260
X-RAY DIFFRACTIONf_plane_restr0.007338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3997-1.42160.3165250.2785533X-RAY DIFFRACTION13
1.4216-1.44490.3515550.253936X-RAY DIFFRACTION23
1.4449-1.46980.3283760.23951569X-RAY DIFFRACTION37
1.4698-1.49660.22141090.19042124X-RAY DIFFRACTION52
1.4966-1.52540.23271350.17722581X-RAY DIFFRACTION62
1.5254-1.55650.22751580.15512722X-RAY DIFFRACTION66
1.5565-1.59030.19411600.1612890X-RAY DIFFRACTION70
1.5903-1.62730.16211530.15952976X-RAY DIFFRACTION72
1.6273-1.6680.17771500.1452891X-RAY DIFFRACTION70
1.668-1.71310.18011470.13662853X-RAY DIFFRACTION69
1.7131-1.76350.19541510.13183148X-RAY DIFFRACTION75
1.7635-1.82050.18491870.12473029X-RAY DIFFRACTION75
1.8205-1.88550.18071460.1263135X-RAY DIFFRACTION75
1.8855-1.9610.14351550.13342993X-RAY DIFFRACTION72
1.961-2.05020.14971530.13382777X-RAY DIFFRACTION67
2.0502-2.15830.17091740.12842962X-RAY DIFFRACTION73
2.1583-2.29350.15091420.12422701X-RAY DIFFRACTION64
2.2935-2.47060.15171440.12172899X-RAY DIFFRACTION70
2.4706-2.71910.17511560.13352796X-RAY DIFFRACTION68
2.7191-3.11240.1581350.13823033X-RAY DIFFRACTION73
3.1124-3.92040.14831550.12943140X-RAY DIFFRACTION76
3.9204-35.33920.15061790.1333761X-RAY DIFFRACTION90

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