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

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Basic information

Entry
Database: PDB / ID: 4wqd
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
GUANIDINE / HEME C / IODIDE ION / Thiosulfate dehydrogenase
Similarity search - Component
Biological speciesAllochromatium vinosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 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 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)28,4507
Polymers26,8691
Non-polymers1,5816
Water4,630257
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-54 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.093, 70.811, 57.873
Angle α, β, γ (deg.)90.00, 128.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1117-

HOH

21A-1164-

HOH

31A-1194-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thiosulfate dehydrogenase / Tetrathionate synthase


Mass: 26869.203 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, 263 molecules

#2: Chemical ChemComp-HEC / HEME C


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


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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-F / 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: 1.22→39.45 Å / Num. obs: 102946 / % possible obs: 91 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 11.39
Reflection shellResolution: 1.22→1.27 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.03 / Num. unique all: 9207 / % possible all: 64

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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: 1.22→39.45 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1832 5101 4.96 %
Rwork0.1514 --
obs0.1529 102775 70.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.22→39.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 100 257 2058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131927
X-RAY DIFFRACTIONf_angle_d1.4852643
X-RAY DIFFRACTIONf_dihedral_angle_d16.536704
X-RAY DIFFRACTIONf_chiral_restr0.061265
X-RAY DIFFRACTIONf_plane_restr0.008346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2211-1.2350.33241430.32072732X-RAY DIFFRACTION59
1.235-1.24950.2971510.30522964X-RAY DIFFRACTION66
1.2495-1.26470.28471510.29473065X-RAY DIFFRACTION66
1.2647-1.28070.31661570.27483156X-RAY DIFFRACTION69
1.2807-1.29760.31490.25233200X-RAY DIFFRACTION69
1.2976-1.31540.28581720.25663098X-RAY DIFFRACTION68
1.3154-1.33420.25861600.24263215X-RAY DIFFRACTION69
1.3342-1.35410.22381610.23143139X-RAY DIFFRACTION69
1.3541-1.37520.25871630.22933051X-RAY DIFFRACTION66
1.3752-1.39780.21072020.2063143X-RAY DIFFRACTION69
1.3978-1.42190.22841630.19163216X-RAY DIFFRACTION71
1.4219-1.44770.22841560.19163281X-RAY DIFFRACTION71
1.4477-1.47560.20411950.18383318X-RAY DIFFRACTION71
1.4756-1.50570.22041710.16553256X-RAY DIFFRACTION72
1.5057-1.53840.20971530.1683179X-RAY DIFFRACTION70
1.5384-1.57420.16821700.15083298X-RAY DIFFRACTION71
1.5742-1.61360.18551720.14253201X-RAY DIFFRACTION70
1.6136-1.65720.18252020.13793230X-RAY DIFFRACTION71
1.6572-1.7060.17881560.13133401X-RAY DIFFRACTION74
1.706-1.76110.14151770.13263397X-RAY DIFFRACTION74
1.7611-1.8240.17211660.13293435X-RAY DIFFRACTION75
1.824-1.8970.20111760.14043409X-RAY DIFFRACTION74
1.897-1.98340.18421510.14493278X-RAY DIFFRACTION71
1.9834-2.0880.17951870.13893294X-RAY DIFFRACTION72
2.088-2.21880.13251950.13423502X-RAY DIFFRACTION76
2.2188-2.39010.19711810.13223431X-RAY DIFFRACTION75
2.3901-2.63060.15771890.13043459X-RAY DIFFRACTION75
2.6306-3.01110.19441730.13773343X-RAY DIFFRACTION73
3.0111-3.79340.16621770.13843567X-RAY DIFFRACTION77
3.7934-45.01270.1571820.13443416X-RAY DIFFRACTION75

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