[English] 日本語
Yorodumi- PDB-1x8i: Crystal Structure of the Zinc Carbapenemase CphA in Complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x8i | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Zinc Carbapenemase CphA in Complex with the Antibiotic Biapenem | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | Aeromonas hydrophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Garau, G. / Dideberg, O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: A Metallo-beta-lactamase Enzyme in Action: Crystal Structures of the Monozinc Carbapenemase CphA and its Complex with Biapenem Authors: Garau, G. / Bebrone, C. / Anne, C. / Galleni, M. / Frere, J.M. / Dideberg, O. #1: Journal: Antimicrob.Agents Chemother. / Year: 2004 Title: Update of the standard numbering scheme for class B beta-lactamases Authors: Garau, G. / Garcia-Saez, I. / Bebrone, C. / Anne, C. / Mercuri, P. / Galleni, M. / Frere, J.M. / Dideberg, O. #2: Journal: Embo J. / Year: 1995 Title: The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold Authors: Carfi, A. / Pares, S. / Duee, E. / Galleni, M. / Duez, C. / Frere, J.M. / Dideberg, O. #3: Journal: J.Mol.Biol. / Year: 2003 Title: Three-dimensional structure of FEZ-1, a monomeric subclass B3 metallo-beta-lactamase from Fluoribacter gormanii, in native form and in complex with D-captopril Authors: Garcia-Saez, I. / Mercuri, P.S. / Papamicael, C. / Kahn, R. / Frere, J.M. / Galleni, M. / Rossolini, G.M. / Dideberg, O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1x8i.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1x8i.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 1x8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/1x8i ftp://data.pdbj.org/pub/pdb/validation_reports/x8/1x8i | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25163.768 Da / Num. of mol.: 1 / Mutation: N220G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: cphA / Plasmid: PUC20-CPHA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(PLYSS) / References: UniProt: P26918, beta-lactamase |
---|
-Non-polymers , 5 types, 197 molecules
#2: Chemical | ChemComp-ZN / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-BMH / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % |
---|---|
Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG, AS, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.54179 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 18, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→26.5 Å / Num. obs: 20636 / % possible obs: 93.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.29 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CphA (N220G) mutant Resolution: 1.9→26.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.37 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.545 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→26.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20 /
|