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Open data
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Basic information
Entry | Database: PDB / ID: 2oz1 | ||||||
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Title | The SoxAX Complex of Rhodovulum Sulfidophilum | ||||||
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![]() | ELECTRON TRANSPORT / ELECTRON TRANSFER / BACTERIAL SULFUR CYCLE / THIOSULFATE OXIDATION / CYSTEINE PERSULFIDE HEME LIGAND / CYTOCHROME C | ||||||
Function / homology | ![]() 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 sulfurtransferase activity / periplasmic space / oxidoreductase activity / electron transfer 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 sulfurtransferase activity / periplasmic space / oxidoreductase activity / electron transfer activity / protein heterodimerization activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kihlken, M.A. / Berks, B.C. / Hemmings, A.M. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 341.4 KB | Display | ![]() |
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PDB format | ![]() | 278.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.5 MB | Display | ![]() |
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Full document | ![]() | 4.6 MB | Display | |
Data in XML | ![]() | 72.6 KB | Display | |
Data in CIF | ![]() | 98.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1h33S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | THE 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 | Mass: 28974.408 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 14756.748 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Chemical | ChemComp-HEC / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.43 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 15, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.774 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.345→2.406 Å / Total num. of bins used: 20
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