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- PDB-1h31: Oxidised SoxAX complex from Rhodovulum sulfidophilum -

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Basic information

Entry
Database: PDB / ID: 1h31
TitleOxidised SoxAX complex from Rhodovulum sulfidophilum
Components
  • CYTOCHROME C
  • DIHEME CYTOCHROME C
KeywordsELECTRON TRANSPORT / SULFUR CYCLE / SOXAX COMPLEX / THIOSULFATE OXIDATION / CYSTEINE PERSULFIDE HEME LIGAND
Function / homology
Function and homology information


sulfide oxidation / L-cysteine S-thiosulfotransferase / oxidoreductase activity, acting on a sulfur group of donors, cytochrome as acceptor / sulfur oxidation / sulfurtransferase activity / cytochrome complex / thiosulfate sulfurtransferase activity / electron transfer activity / periplasmic space / oxidoreductase activity ...sulfide oxidation / L-cysteine S-thiosulfotransferase / oxidoreductase activity, acting on a sulfur group of donors, cytochrome as acceptor / sulfur oxidation / sulfurtransferase activity / cytochrome complex / thiosulfate sulfurtransferase activity / electron transfer activity / periplasmic space / oxidoreductase activity / protein heterodimerization activity / heme binding / metal ion binding
Similarity search - Function
L-cysteine S-thiosulfotransferase subunit SoxA / Sulfur oxidation c-type cytochrome SoxX / SoxA/TsdA, cytochrome c domain / Cytochrome c / 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 / L-cysteine S-thiosulfotransferase subunit SoxA / Cytochrome c
Similarity search - Component
Biological speciesRHODOVULUM SULFIDOPHILUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å
AuthorsBamford, V.A. / Bruno, S. / Rasmussen, T. / Appia-Ayme, C. / Cheesman, M.R. / Berks, B.C. / Hemmings, A.M.
CitationJournal: Embo J. / Year: 2002
Title: Structural Basis for the Oxidation of Thiosulfate by a Sulfur Cycle Enzyme
Authors: Bamford, V.A. / Bruno, S. / Rasmussen, T. / Appia-Ayme, C. / Cheesman, M.R. / Berks, B.C. / Hemmings, A.M.
History
DepositionAug 21, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2002Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHEME CYTOCHROME C
B: CYTOCHROME C
C: DIHEME CYTOCHROME C
D: CYTOCHROME C
E: DIHEME CYTOCHROME C
F: CYTOCHROME C
G: DIHEME CYTOCHROME C
H: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,34720
Polymers174,9258
Non-polymers7,42212
Water12,412689
1
A: DIHEME CYTOCHROME C
B: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5875
Polymers43,7312
Non-polymers1,8563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-12.6 kcal/mol
Surface area20720 Å2
MethodPISA
2
C: DIHEME CYTOCHROME C
D: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5875
Polymers43,7312
Non-polymers1,8563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-14.2 kcal/mol
Surface area20400 Å2
MethodPISA
3
E: DIHEME CYTOCHROME C
F: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5875
Polymers43,7312
Non-polymers1,8563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-15.4 kcal/mol
Surface area20340 Å2
MethodPISA
4
G: DIHEME CYTOCHROME C
H: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5875
Polymers43,7312
Non-polymers1,8563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-13.9 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.188, 102.894, 114.365
Angle α, β, γ (deg.)90.00, 110.45, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.74562, -0.00193, 0.66637), (0.00332, -0.99999, 0.00081), (0.66636, 0.00282, 0.74562)-10.05786, 78.02703, -26.60685
2given(-0.40393, 0.50149, -0.76508), (0.91454, 0.20187, -0.35052), (-0.02134, -0.84128, -0.54018)80.63965, 55.54509, 60.02388
3given(-0.29057, 0.93459, -0.20519), (-0.91224, -0.20587, 0.35417), (0.28876, 0.29009, 0.91239)-30.45963, 73.82, -17.79923

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Components

#1: Protein
DIHEME CYTOCHROME C / SOXA


Mass: 28974.408 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) RHODOVULUM SULFIDOPHILUM (bacteria) / References: UniProt: Q939U1
#2: Protein
CYTOCHROME C / / SOXX


Mass: 14756.748 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) RHODOVULUM SULFIDOPHILUM (bacteria) / References: UniProt: Q939U4
#3: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 689 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 47.8 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 %(w/v)PEG80001reservoir
20.2 Mmagnesium acetate1reservoir
3100 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorDetector: CCD / Date: Jun 15, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. obs: 58706 / % possible obs: 98.2 % / Redundancy: 10 % / Rmerge(I) obs: 0.031
Reflection
*PLUS
Num. measured all: 101074
Reflection shell
*PLUS
% possible obs: 88.7 % / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.55→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 -5 %RANDOM
Rwork0.21 ---
obs0.21 58706 98.2 %-
Refinement stepCycle: LAST / Resolution: 2.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12252 0 516 689 13457
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.298
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.368 / Rfactor Rwork: 0.296

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