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Open data
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Basic information
Entry | Database: PDB / ID: 2wgw | ||||||
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Title | Crystal structure of the OXA-10 V117T mutant at pH 8.0 | ||||||
![]() | (BETA-LACTAMASE OXA-10) x 2 | ||||||
![]() | HYDROLASE / ANTIBIOTIC RESISTANCE / TRANSPOSABLE | ||||||
Function / homology | ![]() penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vercheval, L. / Kerff, F. / Bauvois, C. / Sauvage, E. / Guiet, R. / Charlier, P. / Galleni, M. | ||||||
![]() | ![]() Title: Three Factors that Modulate the Activity of Class D Beta-Lactamases and Interfere with the Post-Translational Carboxylation of Lys70. Authors: Vercheval, L. / Bauvois, C. / Di Paolo, A. / Borel, F. / Ferrer, J.L. / Sauvage, E. / Matagne, A. / Frere, J.M. / Charlier, P. / Galleni, M. / Kerff, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 229.6 KB | Display | ![]() |
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PDB format | ![]() | 183.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.2 KB | Display | ![]() |
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Full document | ![]() | 467.2 KB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 38.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wgvC ![]() 2wkhC ![]() 2wkiC ![]() 1k4fS 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: 27757.514 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||
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#2: Protein | Mass: 27714.512 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | LYS A 70 AND KCX (LYSINE NZ-CARBOXYLIC ACID) A 70 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. IN ...LYS A 70 AND KCX (LYSINE NZ-CARBOXYLIC | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 45.96 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 1.8 M AS BUFFER HEPES 0.1 M PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 16, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979724 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.62 Å / Num. obs: 55385 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 13.45 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 7.7 / % possible all: 94.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1K4F Resolution: 1.8→38.52 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.903 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.102 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.418 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→38.52 Å
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Refine LS restraints |
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