[English] 日本語
Yorodumi- PDB-2rhw: Crystal Structure of the S112A mutant of a C-C hydrolase, BphD fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rhw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3,10-Di-Fluoro HOPDA | ||||||
Components | 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase | ||||||
Keywords | HYDROLASE / C-C bond hydrolase / Aromatic hydrocarbons catabolism | ||||||
Function / homology | Function and homology information 2-hydroxy-6-oxonona-2,4-dienedioate hydrolase activity / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity / : Similarity search - Function | ||||||
Biological species | Burkholderia xenovorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å | ||||||
Authors | Bhowmik, S. / Bolin, J.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: The Molecular Basis for Inhibition of BphD, a C-C Bond Hydrolase Involved in Polychlorinated Biphenyls Degradation: LARGE 3-SUBSTITUENTS PREVENT TAUTOMERIZATION. Authors: Bhowmik, S. / Horsman, G.P. / Bolin, J.T. / Eltis, L.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2rhw.cif.gz | 77.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2rhw.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 2rhw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/2rhw ftp://data.pdbj.org/pub/pdb/validation_reports/rh/2rhw | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31749.268 Da / Num. of mol.: 1 / Mutation: S112A / Source method: isolated from a natural source / Source: (natural) Burkholderia xenovorans (bacteria) / Strain: LB400 / References: UniProt: P47229, EC: 3.7.1.- | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-NA / | ||||
#3: Chemical | #4: Chemical | ChemComp-C0E / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.5 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.9 M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→50 Å / Num. obs: 42640 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.2 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 8.1 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.57→1.63 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 4205 / Rsym value: 50.2 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→27.8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.377 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.081 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.159 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.162 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→27.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.57→1.613 Å / Total num. of bins used: 20
|