+Open data
-Basic information
Entry | Database: PDB / ID: 3ocd | ||||||
---|---|---|---|---|---|---|---|
Title | Diheme SoxAX - C236M mutant | ||||||
Components |
| ||||||
Keywords | Heme-binding protein / Cytochrome / Thiosulfate oxidation pathway / Heme-binding protein-Heme-binding protein complex | ||||||
Function / homology | Function and homology information 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 / periplasmic space / oxidoreductase activity / electron transfer activity / iron ion binding ...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 / periplasmic space / oxidoreductase activity / electron transfer activity / iron ion binding / copper ion binding / protein heterodimerization activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Starkeya novella (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Maher, M.J. | ||||||
Citation | Journal: To be Published Title: Diheme SoxAX proteins - insights into structure and function of the active site Authors: Kilmartin, J. / Maher, M.J. / Krusong, K. / Hanson, G.R. / Bernhardt, P.V. / Riley, M. / Kappler, U. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ocd.cif.gz | 173.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ocd.ent.gz | 137.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ocd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ocd_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ocd_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 3ocd_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 3ocd_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/3ocd ftp://data.pdbj.org/pub/pdb/validation_reports/oc/3ocd | HTTPS FTP |
-Related structure data
Related structure data | 3oa8SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | Heterodimer composed of SoxA and SoxX subunits (chains A and B; chains C and D) |
-Components
#1: Protein | Mass: 30751.395 Da / Num. of mol.: 2 / Mutation: C236M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Starkeya novella (bacteria) / Production host: Rhodobacter capsulatus (bacteria) / References: UniProt: Q7BQR6, UniProt: D7A6E5*PLUS #2: Protein | Mass: 22350.236 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Starkeya novella (bacteria) / Production host: Rhodobacter capsulatus (bacteria) / References: UniProt: Q7BQR5 #3: Chemical | ChemComp-HEC / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.3 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 3350, 0.2M lithium sulfate, 0.1M Tris-HCl pH 8.5, 0.01M spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5412 Å | |||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 2, 2005 | |||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.5412 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
| |||||||||||||||
Reflection | Resolution: 2.25→50 Å / Num. all: 1 / Num. obs: 41134 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | |||||||||||||||
Reflection shell | Resolution: 2.25→2.33 Å / % possible all: 86.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OA8 Resolution: 2.25→41.18 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.904 / SU B: 6.25 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.757 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→41.18 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.249→2.307 Å / Total num. of bins used: 20
|