[English] 日本語
![](img/lk-miru.gif)
- PDB-4c1d: Crystal structure of the metallo-beta-lactamase VIM-2 with L-captopril -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4c1d | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the metallo-beta-lactamase VIM-2 with L-captopril | ||||||
![]() | BETA-LACTAMASE CLASS B VIM-2 | ||||||
![]() | HYDROLASE / ANTIBIOTIC RESISTANCE | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zollman, D. / Brem, J. / McDonough, M.A. / van Berkel, S.S. / Schofield, C.J. | ||||||
![]() | ![]() Title: Structural Basis of Metallo-beta-Lactamase Inhibition by Captopril Stereoisomers. Authors: Brem, J. / van Berkel, S.S. / Zollman, D. / Lee, S.Y. / Gileadi, O. / McHugh, P.J. / Walsh, T.R. / McDonough, M.A. / Schofield, C.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 211.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 169.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 482.2 KB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 35.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bz3C ![]() 4c09C ![]() 4c1cC ![]() 4c1eC ![]() 4c1fC ![]() 4c1gC ![]() 4c1hC ![]() 1ko3S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25693.488 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-240 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 446 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/X8Z.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/X8Z.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
---|---|
Crystal grow | Details: 0.2 M MAGNESIUM FORMATE, 20 % W/V PEG3350, 1 MM TCEP. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 22, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 126706 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 13.24 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.9 / % possible all: 91 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KO3 Resolution: 1.198→39.701 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 18.89 / Stereochemistry target values: ML Details: CONFORMATION OF RAMACHANDRAN OUTLIERS 84 ASP, 87 TRP AND 178 ALA VALIDATED BY CLEAR ELECTRON DENSITY. POSSIBLE ALTERNATIVE CONFORMATION OF LIGAND, HOWEVER VERY LOW OCCUPANCY SO LEFT UNMODELLED.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.198→39.701 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|