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- PDB-4wq7: Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - "a... -

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Basic information

Entry
Database: PDB / ID: 4wq7
TitleThiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - "as isolated" form
ComponentsThiosulfate dehydrogenase
KeywordsOXIDOREDUCTASE / tetrathionate / TsdA / c-type cytochrome / Allochromatium vinosum
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 / Thiosulfate dehydrogenase
Similarity search - Component
Biological speciesAllochromatium vinosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 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, PTDC/BIA-PRO/118535/2010 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 1.3Nov 20, 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiosulfate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6557
Polymers26,9411
Non-polymers1,7146
Water2,936163
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-52 kcal/mol
Surface area10730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.213, 69.883, 57.864
Angle α, β, γ (deg.)90.00, 129.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1123-

HOH

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Components

#1: Protein Thiosulfate dehydrogenase / Tetrathionate synthase


Mass: 26941.332 Da / Num. of mol.: 1
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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D3RVD4, thiosulfate dehydrogenase
#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.: 3 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
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: ALBA / Beamline: XALOC / Wavelength: 1.722 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.722 Å / Relative weight: 1
ReflectionResolution: 1.98→44.81 Å / Num. obs: 29056 / % possible obs: 87 % / Redundancy: 1.8 % / Biso Wilson estimate: 16.75 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5
Reflection shellResolution: 1.98→2.06 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.76 / % possible all: 70

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXphasing
Coot0.7.1model building
PHENIX(phenix.refine: dev_1830)refinement
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.98→44.81 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / Phase error: 18.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1896 1439 4.95 %
Rwork0.1382 --
obs0.1408 29048 87.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.82 Å2
Refinement stepCycle: LAST / Resolution: 1.98→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1707 0 94 163 1964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141887
X-RAY DIFFRACTIONf_angle_d1.5782592
X-RAY DIFFRACTIONf_dihedral_angle_d16.166683
X-RAY DIFFRACTIONf_chiral_restr0.051263
X-RAY DIFFRACTIONf_plane_restr0.008337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9843-2.05520.29181120.19152198X-RAY DIFFRACTION70
2.0552-2.13750.19321440.16882722X-RAY DIFFRACTION86
2.1375-2.23480.23311410.15762704X-RAY DIFFRACTION86
2.2348-2.35260.22461450.14542775X-RAY DIFFRACTION88
2.3526-2.50.19841470.13412837X-RAY DIFFRACTION88
2.5-2.6930.1841470.12882814X-RAY DIFFRACTION90
2.693-2.9640.20881480.13542867X-RAY DIFFRACTION91
2.964-3.39280.15991490.13912873X-RAY DIFFRACTION91
3.3928-4.27410.15891520.12122892X-RAY DIFFRACTION91
4.2741-46.11490.18261540.13112927X-RAY DIFFRACTION92

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