[English] 日本語
Yorodumi- PDB-4c4b: Superoxide reductase (Neelaredoxin) from Archaeoglobus fulgidus E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c4b | ||||||
---|---|---|---|---|---|---|---|
Title | Superoxide reductase (Neelaredoxin) from Archaeoglobus fulgidus E12V in the reduced form | ||||||
Components | SUPEROXIDE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / OXYGEN DETOXIFICATION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ARCHAEOGLOBUS FULGIDUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Bandeiras, T.M. / Rodrigues, J.V. / Sousa, C.M. / Barradas, A.R. / Pinho, F.G. / Pinto, A.F. / Teixeira, M. / Matias, P.M. / Romao, C.V. | ||||||
Citation | Journal: To be Published Title: Understanding the Role of Key Residues in the Superoxide Reductase Molecular Mechanism, Exploring Archaeoglobus Fulgidus Sor Structure Authors: Bandeiras, T.M. / Rodrigues, J.V. / Sousa, C.M. / Barradas, A.R. / Pinho, F.G. / Pinto, A.F. / Teixeira, M. / Matias, P.M. / Romao, C.V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4c4b.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4c4b.ent.gz | 86.4 KB | Display | PDB format |
PDBx/mmJSON format | 4c4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c4b_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4c4b_full_validation.pdf.gz | 436.7 KB | Display | |
Data in XML | 4c4b_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 4c4b_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/4c4b ftp://data.pdbj.org/pub/pdb/validation_reports/c4/4c4b | HTTPS FTP |
-Related structure data
Related structure data | 4bffC 4bfjC 4bfkC 4c4uC 4bglS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13682.566 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Plasmid: PT7-7/NAFE12VA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: O29903 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72 % / Description: NONE |
---|---|
Crystal grow | pH: 7 / Details: 0.1 M HEPES PH 7.0 AND 26% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 30, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→41.84 Å / Num. obs: 17359 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 45.66 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BGL Resolution: 2.5→40.477 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 20.61 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→40.477 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|