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- PDB-1x8i: Crystal Structure of the Zinc Carbapenemase CphA in Complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1x8i | ||||||
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Title | Crystal Structure of the Zinc Carbapenemase CphA in Complex with the Antibiotic Biapenem | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Garau, G. / Dideberg, O. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.4 KB | Display | ![]() |
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PDB format | ![]() | 47.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 784.7 KB | Display | ![]() |
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Full document | ![]() | 785.2 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 197 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BMH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BMH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-BMH / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % |
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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 |
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Diffraction source | Source: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refinement step | Cycle: LAST / Resolution: 1.9→26.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20 /
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