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- PDB-2nyp: Structure of beta-lactamase II from Bacillus cereus. R121H, C221D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2nyp | ||||||
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Title | Structure of beta-lactamase II from Bacillus cereus. R121H, C221D doble mutant with two zinc ions. | ||||||
![]() | Beta-lactamase II | ||||||
![]() | HYDROLASE / Beta-lactamase II / Bacillus cereus | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Medrano Martin, F.J. / Vila, A.J. / Gonzalez, J.M. | ||||||
![]() | ![]() Title: The Zn2 position in metallo-beta-lactamases is critical for activity: a study on chimeric metal sites on a conserved protein scaffold. Authors: Gonzalez, J.M. / Medrano Martin, F.J. / Costello, A.L. / Tierney, D.L. / Vila, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.7 KB | Display | ![]() |
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PDB format | ![]() | 43.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.6 KB | Display | ![]() |
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Full document | ![]() | 432.2 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nxaC ![]() 2nzeC ![]() 2nzfC ![]() 1bc2S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24286.621 Da / Num. of mol.: 1 / Mutation: y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.1 M sodium cacodylate,60 mM sodium tartrate, 18% PEG 3350, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 14, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.42 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→50 Å / Num. obs: 18461 / % possible obs: 97.6 % / Observed criterion σ(I): 45536 / Redundancy: 2.6 % / Rsym value: 0.047 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.84→1.91 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.277 / % possible all: 86.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1bc2 Resolution: 1.84→68.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.271 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.794 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→68.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.841→1.889 Å / Total num. of bins used: 20
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