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Yorodumi- PDB-2pu5: Crystal Structure of a C-C bond hydrolase, BphD, from Burkholderi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pu5 | ||||||
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Title | Crystal Structure of a C-C bond hydrolase, BphD, from Burkholderia xenovorans LB400 | ||||||
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 / : Similarity search - Function | ||||||
Biological species | Burkholderia xenovorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 2pu5.cif.gz | 125.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pu5.ent.gz | 99.6 KB | Display | PDB format |
PDBx/mmJSON format | 2pu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/2pu5 ftp://data.pdbj.org/pub/pdb/validation_reports/pu/2pu5 | 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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Details | The biological assembly is a tetramer generated from the dimer in the asymmetric unit related by the crystallographic two fold axis. |
-Components
#1: Protein | Mass: 32068.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: bphD / Production host: Escherichia coli (E. coli) / References: UniProt: P47229, EC: 3.7.1.- #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2.0 M sodium, malonate, pH 6.0 or 6.5, 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: 2.3→50 Å / Num. obs: 30870 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rsym value: 12.4 / Net I/σ(I): 12.2 |
Reflection shell | Highest resolution: 2.3 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 3046 / Rsym value: 33.2 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.898 / Highest resolution: 2.3 Å / SU B: 7.07 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.252 / 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: 48.757 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.358 Å / Total num. of bins used: 20
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