[English] 日本語
![](img/lk-miru.gif)
- PDB-3m6b: Crystal Structure of the Ertapenem Pre-isomerized Covalent Adduct... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3m6b | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Ertapenem Pre-isomerized Covalent Adduct with TB B-lactamase | ||||||
![]() | Beta-lactamase | ||||||
![]() | Hydrolase/Antibiotic / alpha-beta structure / Antibiotic resistance / Cell membrane / Hydrolase / Lipoprotein / Membrane / Palmitate / Hydrolase-Antibiotic complex | ||||||
Function / homology | ![]() : / : / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tremblay, L.W. / Fan, F. / Blanchard, J.S. | ||||||
![]() | ![]() Title: Biochemical and structural characterization of Mycobacterium tuberculosis beta-lactamase with the carbapenems ertapenem and doripenem. Authors: Tremblay, L.W. / Fan, F. / Blanchard, J.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 127.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 97.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3iqaC ![]() 3m6hC ![]() 3dwzS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 28272.721 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0C5C1, UniProt: P9WKD3*PLUS, beta-lactamase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.41 % |
---|---|
Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 4.1 Details: 0.1 M HEPES, 2 M NH4(H2)PO4, pH 4.1, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 21, 2010 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 63485 / Num. obs: 63485 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.3→1.33 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4388 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdb entry 3DWZ Resolution: 1.3→26.28 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.384 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.73 Å2 / Biso mean: 13.287 Å2 / Biso min: 4.58 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→26.28 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
|