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Yorodumi- PDB-2jap: Clavulanic Acid Dehydrogenase: Structural and Biochemical Analysi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jap | ||||||
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Title | Clavulanic Acid Dehydrogenase: Structural and Biochemical Analysis of the Final Step in the Biosynthesis of the beta-Lactamase Inhibitor Clavulanic acid | ||||||
Components | CLAVALDEHYDE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / ANTIBIOTIC BIOSYNTHESIS / BETA-LACTAMASE INHIBITOR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOMYCES CLAVULIGERUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å | ||||||
Authors | MacKenzie, A.K. / Kershaw, N.J. / Hernandez, H. / Robinson, C.V. / Schofield, C.J. / Andersson, I. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Clavulanic Acid Dehydrogenase: Structural and Biochemical Analysis of the Final Step in the Biosynthesis of the Beta-Lactamase Inhibitor Clavulanic Acid Authors: Mackenzie, A.K. / Kershaw, N.J. / Hernandez, H. / Robinson, C.V. / Schofield, C.J. / Andersson, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jap.cif.gz | 190.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jap.ent.gz | 162.4 KB | Display | PDB format |
PDBx/mmJSON format | 2jap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/2jap ftp://data.pdbj.org/pub/pdb/validation_reports/ja/2jap | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 26357.094 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Strain: NRRL3585 / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LCV7 #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-J01 / ( #4: 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: 2.2 Å3/Da / Density % sol: 42.5 % Description: SELENOMETHIONINE STRUCTURE USED FOR RIGID BODY REFINEMENT WITH ISOMORPHOUS CRYSTALS |
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Crystal grow | pH: 6.5 Details: 25% PEG 2000,MONOMETHYL ETHER, 0.8 M SODIUM FORMATE, 0.1 M CACODYLATE BUFFER (PH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.979 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 19, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→34.9 Å / Num. obs: 53663 / % possible obs: 99.4 % / Observed criterion σ(I): 6 / Redundancy: 4.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.1→2.1 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.4 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.1→34.86 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 10.618 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.182 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→34.86 Å
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Refine LS restraints |
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