[English] 日本語
![](img/lk-miru.gif)
- PDB-4c1e: Crystal structure of the metallo-beta-lactamase VIM-2 with D-captopril -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4c1e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the metallo-beta-lactamase VIM-2 with D-captopril | ||||||
![]() | BETA-LACTAMASE CLASS B VIM-2 | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() antibiotic catabolic process / ![]() ![]() ![]() 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 | ![]() | 217.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 174.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4bz3C ![]() 4c09C ![]() 4c1cC ![]() 4c1dC ![]() 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 27-266 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 549 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/MCO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MCO.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 / | ![]() |
---|
-Details
Nonpolymer details | ((S)-3-MERCAPTO-2-METHYLPROP |
---|
-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: RIGAKU CCD / Detector: CCD / Date: Oct 17, 2012 / Details: VARIMAX HF |
Radiation | Monochromator: CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.4→50 Å / Num. obs: 78943 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 13.46 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 95.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1KO3 Resolution: 1.399→31.21 Å / SU ML: 0.13 / σ(F): 1.33 / Phase error: 17 / Stereochemistry target values: ML Details: CONFORMATION OF RAMACHANDRAN OUTLIERS 84 ASP, 87 TRP AND 178 ALA VALIDATED BY CLEAR ELECTRON DENSITY.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.399→31.21 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|