[English] 日本語
Yorodumi- PDB-4pm5: Crystal structure of CTX-M-14 S70G beta-lactamase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pm5 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of CTX-M-14 S70G beta-lactamase in complex with cefotaxime at 1.26 Angstroms resolution | |||||||||
Components | Beta-lactamase CTX-M-14 | |||||||||
Keywords | HYDROLASE/ANTIBIOTIC / Class A beta-lactamase / cefotaxime / HYDROLASE-ANTIBIOTIC complex | |||||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | |||||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.261 Å | |||||||||
Authors | Adamski, C.J. / Cardenas, A.M. / Sankaran, B. / Palzkill, T. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Molecular Basis for the Catalytic Specificity of the CTX-M Extended-Spectrum beta-Lactamases. Authors: Adamski, C.J. / Cardenas, A.M. / Brown, N.G. / Horton, L.B. / Sankaran, B. / Prasad, B.V. / Gilbert, H.F. / Palzkill, T. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4pm5.cif.gz | 76 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4pm5.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 4pm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/4pm5 ftp://data.pdbj.org/pub/pdb/validation_reports/pm/4pm5 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4pm6C 4pm7C 4pm8C 4pm9C 4pmaC 1yltS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27970.520 Da / Num. of mol.: 1 / Fragment: UNP residues 29-291 / Mutation: S70G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria) Strain: HS11286 / Gene: KPHS_p301310 / Production host: Escherichia coli (E. coli) / References: UniProt: G8XD06, UniProt: A0A0H3H219*PLUS | ||
---|---|---|---|
#2: Chemical | ChemComp-CE3 / ( | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.65 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: Ammonium phosphate, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→29.5 Å / Num. obs: 61202 / % possible obs: 99.7 % / Redundancy: 2 % / Net I/σ(I): 19.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YLT Resolution: 1.261→29.451 Å / SU ML: 0.1 / Cross valid method: NONE / σ(F): 1.93 / Phase error: 16.45 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.261→29.451 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|