[English] 日本語
![](img/lk-miru.gif)
- PDB-2jah: Biochemical and structural analysis of the Clavulanic acid dehyde... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2jah | ||||||
---|---|---|---|---|---|---|---|
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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 197.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 169.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 41.6 KB | Display | |
Data in CIF | ![]() | 58.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-
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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
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. |
---|---|
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 |
---|---|
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 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|