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Yorodumi- PDB-2rht: Crystal Structure of the S112A mutant of a C-C hydrolase, BphD fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rht | ||||||
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Title | Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3-Cl 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: 1.7 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rht.cif.gz | 76.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rht.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 2rht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rht_validation.pdf.gz | 704.3 KB | Display | wwPDB validaton report |
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Full document | 2rht_full_validation.pdf.gz | 706.9 KB | Display | |
Data in XML | 2rht_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 2rht_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/2rht ftp://data.pdbj.org/pub/pdb/validation_reports/rh/2rht | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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.- |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-C1E / ( |
#4: Chemical | ChemComp-MLI / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.07 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→83.33 Å / Num. obs: 33456 / % possible obs: 99.56 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Biso Wilson estimate: 20.3 Å2 / Rsym value: 6.6 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 3297 / Rsym value: 49.2 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→83.33 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.696 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 21.065 Å2
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Refine analyze | Luzzati coordinate error obs: 0.157 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→83.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.746 Å / Total num. of bins used: 20
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