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Yorodumi- PDB-2ri6: Crystal Structure of S112A mutant of a C-C hydrolase, BphD from B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ri6 | |||||||||
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Title | Crystal Structure of S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400 | |||||||||
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 / Resolution: 1.68 Å | |||||||||
Authors | Bhowmik, S. / Bolin, J.T. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: The tautomeric half-reaction of BphD, a C-C bond hydrolase. Kinetic and structural evidence supporting a key role for histidine 265 of the catalytic triad. Authors: Horsman, G.P. / Bhowmik, S. / Seah, S.Y. / Kumar, 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 | 2ri6.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ri6.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ri6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/2ri6 ftp://data.pdbj.org/pub/pdb/validation_reports/ri/2ri6 | HTTPS FTP |
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-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 | #4: 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: 2.36 Å3/Da / Density % sol: 47.98 % |
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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: Jun 4, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→50 Å / Num. obs: 34855 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.3 % / Rsym value: 12.6 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.68→1.74 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 8.1 / Num. unique all: 3424 / Rsym value: 27.1 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Resolution: 1.68→44.95 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.825 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.093 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.094 Å2
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Refine analyze | Luzzati coordinate error obs: 0.173 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→44.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.723 Å / Total num. of bins used: 20
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