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- PDB-2oz1: The SoxAX Complex of Rhodovulum Sulfidophilum -

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Basic information

Entry
Database: PDB / ID: 2oz1
TitleThe SoxAX Complex of Rhodovulum Sulfidophilum
Components
  • Cytochrome c
  • Diheme cytochrome c
KeywordsELECTRON TRANSPORT / ELECTRON TRANSFER / BACTERIAL SULFUR CYCLE / THIOSULFATE OXIDATION / CYSTEINE PERSULFIDE HEME LIGAND / CYTOCHROME C
Function / homology
Function and homology information


L-cysteine S-thiosulfotransferase / oxidoreductase activity, acting on a sulfur group of donors, cytochrome as acceptor / sulfide oxidation / sulfur oxidation / sulfurtransferase activity / cytochrome complex / thiosulfate-cyanide sulfurtransferase activity / periplasmic space / electron transfer activity / oxidoreductase activity ...L-cysteine S-thiosulfotransferase / oxidoreductase activity, acting on a sulfur group of donors, cytochrome as acceptor / sulfide oxidation / sulfur oxidation / sulfurtransferase activity / cytochrome complex / thiosulfate-cyanide sulfurtransferase activity / periplasmic space / electron transfer activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKihlken, M.A. / Berks, B.C. / Hemmings, A.M.
CitationJournal: To be Published
Title: The crystal structure of recombinant Rhodovulum sulfidophilum SoxAX confirms cysteine persulfide coordination to the catalytic heme
Authors: Kihlken, M.A. / Berks, B.C. / Hemmings, A.M.
History
DepositionFeb 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 13, 2024Group: Structure summary / Category: 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: 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
Water16,916939
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
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
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
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
Unit cell
Length a, b, c (Å)80.975, 102.949, 115.706
Angle α, β, γ (deg.)90.00, 110.22, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE BIOLOGICAL ASSEMBLY IS A SOXAX HETERODIMER. THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS FOUR INDEPENDENT COPIES OF THE BIOLOGICAL ASSEMBLY.

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Components

#1: Protein
Diheme cytochrome c


Mass: 28974.408 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodovulum sulfidophilum (bacteria) / Strain: 1374T / Gene: soxA / Plasmid: pMKS12 / Production host: Rhodobacter capsulatus (bacteria) / Strain (production host): 37B4DELTADORA / References: UniProt: Q939U1
#2: Protein
Cytochrome c


Mass: 14756.748 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodovulum sulfidophilum (bacteria) / Strain: 1374T / Gene: soxX / Plasmid: pMKS12 / Production host: Rhodobacter capsulatus (bacteria) / Strain (production host): 37B4DELTADORA / References: UniProt: Q939U4
#3: Chemical
ChemComp-HEC / HEME C


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


Mass: 18.015 Da / Num. of mol.: 939 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% (w/v) PEG 4K, 0.2 M magnesium acetate, 100 mM sodium MES buffer pH 6.5. The crystals could be cryoprotected by transferring them to stabilization solution containing 25% (v/v) ethylene ...Details: 15% (w/v) PEG 4K, 0.2 M magnesium acetate, 100 mM sodium MES buffer pH 6.5. The crystals could be cryoprotected by transferring them to stabilization solution containing 25% (v/v) ethylene glycol. , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 15, 2005
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.345→108.577 Å / Num. all: 71803 / Num. obs: 71803 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.34-2.471.50.1893.71332688670.18981.5
2.47-2.622.80.1873.928252101850.18798.9
2.62-2.82.90.1445.12764395860.14499.4
2.8-3.032.90.1146.32597189650.11499.2
3.03-3.312.90.0927.72387482110.09298.9
3.31-3.712.90.0729.22156974120.07298.5
3.71-4.282.90.05910.61898965350.05998.3
4.28-5.242.90.0589.91586954850.05897.7
5.24-7.412.90.0619.41221742390.06196.9
7.41-54.312.70.0657.5627923180.06595.4

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
DNAdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H33

1h33


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.868 / SU B: 7.203 / SU ML: 0.175 / Isotropic thermal model: INDIVIDUAL ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.455 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3633 5.1 %RANDOM
Rwork0.187 ---
all0.189 71773 --
obs0.189 71773 96.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.774 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20.44 Å2
2---0.18 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12213 0 516 939 13668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213084
X-RAY DIFFRACTIONr_angle_refined_deg1.3312.0817942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84751583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34123.154596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.596151929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.34915124
X-RAY DIFFRACTIONr_chiral_restr0.0820.21824
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210356
X-RAY DIFFRACTIONr_nbd_refined0.2310.26732
X-RAY DIFFRACTIONr_nbtor_refined0.2980.28840
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.21038
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.219
X-RAY DIFFRACTIONr_mcbond_it0.5411.58141
X-RAY DIFFRACTIONr_mcangle_it0.814212717
X-RAY DIFFRACTIONr_scbond_it1.30535788
X-RAY DIFFRACTIONr_scangle_it2.0784.55201
LS refinement shellResolution: 2.345→2.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 191 -
Rwork0.219 3739 -
obs-3930 71.74 %

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