+Open data
-Basic information
Entry | Database: PDB / ID: 3nck | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of BlaC-E166A covalently bound with Nafcillin | ||||||
Components | Beta-lactamase | ||||||
Keywords | Hydrolase/Antibiotic / penicillin binding protein / beta-lactam covalent adduct / Hydrolase-Antibiotic complex | ||||||
Function / homology | Function and homology information : / : / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Tremblay, L.W. / Blanchard, J.S. | ||||||
Citation | Journal: To be Published Title: BlaC-E166A covalently bound with cephalosporins and penicillins Authors: Tremblay, L.W. / Blanchard, J.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3nck.cif.gz | 63.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3nck.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 3nck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/3nck ftp://data.pdbj.org/pub/pdb/validation_reports/nc/3nck | HTTPS FTP |
---|
-Related structure data
Related structure data | 3nblC 3nc8C 3ndeC 3ndgC 3dwzS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28214.689 Da / Num. of mol.: 1 / Mutation: E182A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaA, blaC, MT2128, MTCY49.07c, Rv2068c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 References: UniProt: P0C5C1, UniProt: P9WKD3*PLUS, beta-lactamase |
---|---|
#2: Chemical | ChemComp-NFF / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.13 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, 2 M NH4H2PO4, pH 7.5, Vapor diffusion, Sitting drop, temperature 298K |
-Data collection
Diffraction |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||
Detector |
| |||||||||||||||
Radiation |
| |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.8→50.79 Å / Num. obs: 6626 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 12.1 | |||||||||||||||
Reflection shell | Resolution: 2.8→2.874 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 1.9 / Num. unique all: 327 / % possible all: 93.89 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DWZ Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.872 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.766 / SU ML: 0.314 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.424 / 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: 68.4 Å2 / Biso mean: 34.813 Å2 / Biso min: 13.94 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.874 Å / Total num. of bins used: 20
|