[English] 日本語
Yorodumi- PDB-3pm5: Crystal Structure of BoxB in mixed valent state with bound benzoyl-CoA -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pm5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of BoxB in mixed valent state with bound benzoyl-CoA | ||||||
Components | Benzoyl-CoA oxygenase component B | ||||||
Keywords | OXIDOREDUCTASE / diiron center / epoxidase / benzoyl coenzyme A | ||||||
Function / homology | Function and homology information benzoyl-CoA 2,3-epoxidase / phenylacetate catabolic process / dioxygenase activity / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Azoarcus evansii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Weinert, T. / Rather, L. / Fuchs, G. / Ermler, U. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structure and Mechanism of the Diiron Benzoyl-Coenzyme A Epoxidase BoxB. Authors: Rather, L.J. / Weinert, T. / Demmer, U. / Bill, E. / Ismail, W. / Fuchs, G. / Ermler, U. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3pm5.cif.gz | 786.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3pm5.ent.gz | 656.8 KB | Display | PDB format |
PDBx/mmJSON format | 3pm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pm5_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3pm5_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3pm5_validation.xml.gz | 75.6 KB | Display | |
Data in CIF | 3pm5_validation.cif.gz | 103.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/3pm5 ftp://data.pdbj.org/pub/pdb/validation_reports/pm/3pm5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 55668.227 Da / Num. of mol.: 4 / Fragment: BoxB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azoarcus evansii (bacteria) / Gene: Azoarcus evansii, boxB / Production host: Azoarcus evansii (bacteria) / References: UniProt: Q9AIX7, EC: 1.14.12.21 |
---|
-Non-polymers , 8 types, 659 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-PGO / #6: Chemical | ChemComp-BYC / #7: Chemical | #8: Chemical | ChemComp-PGE / | #9: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | THE C-TERMINAL TAGGED BOXB WAS INTEGRATED INTO THE GENOME OF AZOARCUS EVANSII AS DESCRIBED ...THE C-TERMINAL TAGGED BOXB WAS INTEGRATED |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.19 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 10% PEG 4000, 0.1M sodium acetate, 0.1M Li2SO4, 18% glycerol, 5 mM benzoyl-CoA, 1 mM NADPH, 0.1 mg/ml BoxA 10 mM Pipes, 0.1 M KCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.2137 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2010 |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2137 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.4 Å / Num. all: 98025 / Num. obs: 98025 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.3→2.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.475 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 12.945 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.221 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.196 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→49.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|