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- PDB-2jah: Biochemical and structural analysis of the Clavulanic acid dehyde... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jah | ||||||
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Title | Biochemical and structural analysis of the Clavulanic acid dehydeogenase (CAD) from Streptomyces clavuligerus | ||||||
![]() | CLAVULANIC ACID DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / LACTAMASE INHIBITOR / ANTIBIOTIC BIOSYNTHESIS / NADPH / CLAVULANIC ACID | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | MacKenzie, A.K. / Kershaw, N.J. / Hernandez, H. / Robinson, C.V. / Schofield, C.J. / Andersson, I. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.7 KB | Display | ![]() |
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PDB format | ![]() | 169.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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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: 26685.359 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NDP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 42.7 % Description: THE PDB ENTRY 1NFF WAS USED AS A MODEL TO ASSIST BUILDING. |
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Crystal grow | pH: 6.5 Details: 10% PEG 1000, 10% PEG 8000, 0.3 M SODIUM ACETATE, 0.05 M BIS-TRIS BUFFER (PH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 24, 2004 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND, GE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29.92 Å / Num. obs: 82024 / % possible obs: 96.2 % / Observed criterion σ(I): 6 / Redundancy: 5.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.7 / % possible all: 80.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.8→29.92 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.765 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NO ELECTRON DENSITY COULD BE OBSERVER FOR MET 1
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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: 23.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→29.92 Å
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Refine LS restraints |
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