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- PDB-4wq9: Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - di... -

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Basic information

Entry
Database: PDB / ID: 4wq9
TitleThiosulfate dehydrogenase (TsdA) from Allochromatium vinosum - dithionite soak
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
HYDROSULFURIC ACID / HEME C / IODIDE ION / THIOSULFATE / Thiosulfate dehydrogenase
Similarity search - Component
Biological speciesAllochromatium vinosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Sep 8, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_special_symmetry.auth_seq_id / _struct_ref_seq_dif.details / _struct_site_gen.auth_seq_id
Revision 2.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)28,7689
Polymers26,9731
Non-polymers1,7958
Water4,216234
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-64 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.289, 69.864, 57.805
Angle α, β, γ (deg.)90.00, 129.42, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1178-

HOH

21A-1195-

HOH

31A-1283-

HOH

41A-1315-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thiosulfate dehydrogenase / Tetrathionate synthase


Mass: 26973.332 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 BL21(DE3) (bacteria) / References: UniProt: D3RVD4, thiosulfate dehydrogenase

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Non-polymers , 7 types, 242 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.: 2 / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#7: Chemical ChemComp-THJ / THIOSULFATE


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


Mass: 18.015 Da / Num. of mol.: 234 / 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: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.2395 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2395 Å / Relative weight: 1
ReflectionResolution: 1.47→34.96 Å / Num. obs: 66925 / % possible obs: 93 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.01
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.93 / Num. unique all: 5738 / % possible all: 86

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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: 1.47→34.96 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 18.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1785 3272 4.9 %
Rwork0.1402 --
obs0.1421 66843 82.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 0 103 234 2064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181921
X-RAY DIFFRACTIONf_angle_d1.5242632
X-RAY DIFFRACTIONf_dihedral_angle_d16.262693
X-RAY DIFFRACTIONf_chiral_restr0.073266
X-RAY DIFFRACTIONf_plane_restr0.007342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4704-1.49240.3121030.28692254X-RAY DIFFRACTION66
1.4924-1.51570.30471180.25052419X-RAY DIFFRACTION73
1.5157-1.54050.2636970.22232774X-RAY DIFFRACTION81
1.5405-1.56710.23441410.18982718X-RAY DIFFRACTION81
1.5671-1.59560.24321490.18592762X-RAY DIFFRACTION82
1.5956-1.62630.231500.17532807X-RAY DIFFRACTION84
1.6263-1.65950.22151530.16522843X-RAY DIFFRACTION84
1.6595-1.69560.18811600.152849X-RAY DIFFRACTION85
1.6956-1.7350.16881610.14062820X-RAY DIFFRACTION86
1.735-1.77840.18051550.12992932X-RAY DIFFRACTION86
1.7784-1.82650.19611290.13372866X-RAY DIFFRACTION84
1.8265-1.88020.2061360.13842845X-RAY DIFFRACTION84
1.8802-1.94090.18561580.1372880X-RAY DIFFRACTION86
1.9409-2.01030.19241470.13772751X-RAY DIFFRACTION82
2.0103-2.09080.18441350.13052701X-RAY DIFFRACTION80
2.0908-2.1860.14321540.12452781X-RAY DIFFRACTION82
2.186-2.30120.14321510.11872897X-RAY DIFFRACTION86
2.3012-2.44540.16771490.11982775X-RAY DIFFRACTION83
2.4454-2.63410.17771420.12752819X-RAY DIFFRACTION83
2.6341-2.89920.20281600.1382709X-RAY DIFFRACTION81
2.8992-3.31860.15311550.14112858X-RAY DIFFRACTION85
3.3186-4.18060.15051450.12322934X-RAY DIFFRACTION87
4.1806-44.36260.16661240.13622577X-RAY DIFFRACTION76

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