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

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Basic information

Entry
Database: PDB / ID: 4wqc
TitleThiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - K208N 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 / THIOSULFATE / Thiosulfate dehydrogenase
Similarity search - Component
Biological speciesAllochromatium vinosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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
Revision 2.0May 8, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)28,4967
Polymers26,9261
Non-polymers1,5696
Water4,450247
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-54 kcal/mol
Surface area10690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.054, 71.034, 57.811
Angle α, β, γ (deg.)90.00, 129.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1108-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thiosulfate dehydrogenase / Tetrathionate synthase


Mass: 26926.254 Da / Num. of mol.: 1 / Mutation: K208N
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 , 5 types, 253 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-THJ / THIOSULFATE


Mass: 112.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O3S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: Diamond / Beamline: I02 / Wavelength: 0.954 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.56→39.44 Å / Num. obs: 33997 / % possible obs: 96 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.12
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.42 / % possible all: 90

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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: 1.56→39.44 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2005 1700 5.01 %
Rwork0.1459 --
obs0.1486 33944 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.56→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 104 247 2065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121936
X-RAY DIFFRACTIONf_angle_d1.4772658
X-RAY DIFFRACTIONf_dihedral_angle_d16.765707
X-RAY DIFFRACTIONf_chiral_restr0.04268
X-RAY DIFFRACTIONf_plane_restr0.007347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.561-1.60690.34081300.27272453X-RAY DIFFRACTION88
1.6069-1.65880.29251400.25022662X-RAY DIFFRACTION96
1.6588-1.71810.30281420.21232676X-RAY DIFFRACTION96
1.7181-1.78680.27441410.19162690X-RAY DIFFRACTION97
1.7868-1.86820.25951420.17432691X-RAY DIFFRACTION97
1.8682-1.96670.21731430.15152703X-RAY DIFFRACTION96
1.9667-2.08990.19511410.14732686X-RAY DIFFRACTION97
2.0899-2.25120.2121420.13242697X-RAY DIFFRACTION97
2.2512-2.47780.20451440.13042729X-RAY DIFFRACTION97
2.4778-2.83630.18011440.13342745X-RAY DIFFRACTION98
2.8363-3.57320.19491460.13432761X-RAY DIFFRACTION98
3.5732-44.63170.15211450.12652751X-RAY DIFFRACTION97

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