[English] 日本語
Yorodumi- PDB-1xuq: Crystal Structure of SodA-1 (BA4499) from Bacillus anthracis at 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xuq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of SodA-1 (BA4499) from Bacillus anthracis at 1.8A Resolution. | ||||||
Components | Superoxide dismutase | ||||||
Keywords | OXIDOREDUCTASE / SodA-1 / Superoxide dismutase / Bacillus anthracis / BA4499 / SPINE | ||||||
Function / homology | Function and homology information superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Boucher, I.W. / Levdikov, V.M. / Blagova, E.V. / Fogg, M.J. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Structures of two superoxide dismutases from Bacillus anthracis reveal a novel active centre. Authors: Boucher, I.W. / Kalliomaa, A.K. / Levdikov, V.M. / Blagova, E.V. / Fogg, M.J. / Brannigan, J.A. / Wilson, K.S. / Wilkinson, A.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1xuq.cif.gz | 103.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1xuq.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xuq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xuq_validation.pdf.gz | 435.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1xuq_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 1xuq_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 1xuq_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/1xuq ftp://data.pdbj.org/pub/pdb/validation_reports/xu/1xuq | HTTPS FTP |
-Related structure data
Related structure data | 1xreC 1jr9S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23750.092 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: sodA1, sodA-1 / Plasmid: pET-YSBLIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q81LW0, superoxide dismutase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.7 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG4000, Sodium Acetate trihydrate, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2004 / Details: Rh coated Si mirror |
Radiation | Monochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 39919 / Num. obs: 39919 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3607 / % possible all: 89.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JR9 Resolution: 1.8→31.45 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.028 / SU ML: 0.094 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.123 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 24.884 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→31.45 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
|