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Yorodumi- PDB-2puh: Crystal Structure of the S112A mutant of a C-C hydrolase, BphD fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2puh | ||||||
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Title | Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with its substrate HOPDA | ||||||
Components | 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase | ||||||
Keywords | HYDROLASE / C-C bond hydrolase / Structural Genomics | ||||||
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 / aromatic compound catabolic process Similarity search - Function | ||||||
Biological species | Burkholderia xenovorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 | 2puh.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2puh.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 2puh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/2puh ftp://data.pdbj.org/pub/pdb/validation_reports/pu/2puh | HTTPS FTP |
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-Related structure data
Related structure data | 2pu5C 2pu7C 2pujC 2ri6C 2og1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: x, y, z; -x+1/2, -y+1/2, z+1/2; -y, x+1/2, z+1/4; y+1/2, -x, z+3/4; |
-Components
#1: Protein | Mass: 32052.648 Da / Num. of mol.: 1 / Mutation: S112A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Gene: bphD / Production host: Escherichia coli (E. coli) / References: UniProt: P47229, EC: 3.7.1.- |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-MLI / |
#4: Chemical | ChemComp-HPK / ( |
#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: 2.33 Å3/Da / Density % sol: 47.2 % |
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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: 21-ID-D / 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: 1.82→82.5 Å / Num. obs: 27213 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rsym value: 5.4 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 1.82→1.868 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 2538 / Rsym value: 45.1 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OG1 Resolution: 1.82→82.48 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.732 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.115 / 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: 31.5 Å2
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Refine analyze | Luzzati coordinate error obs: 0.199 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→82.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.868 Å / Total num. of bins used: 20
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