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Open data
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Basic information
Entry | Database: PDB / ID: 2hp6 | ||||||
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Title | Crystal structure of the OXA-10 W154A mutant at pH 7.5 | ||||||
![]() | Beta-lactamase PSE-2 | ||||||
![]() | HYDROLASE / class D beta-lactamase / lysine carboxylation | ||||||
Function / homology | ![]() penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kerff, F. / Falzone, C. / Herman, R. / Sauvage, E. / Charlier, P. | ||||||
![]() | ![]() Title: Critical role of tryptophan 154 for the activity and stability of class D beta-lactamases. Authors: Baurin, S. / Vercheval, L. / Bouillenne, F. / Falzone, C. / Brans, A. / Jacquamet, L. / Ferrer, J.L. / Sauvage, E. / Dehareng, D. / 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 | ![]() | 116 KB | Display | ![]() |
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PDB format | ![]() | 89.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.9 KB | Display | ![]() |
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Full document | ![]() | 448.7 KB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2hp5C ![]() 2hp9C ![]() 2hpbC ![]() 2rl3C ![]() 2wgiC ![]() 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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Details | The biological assembly is a dimer, composed from the two monomers A and B present in the asymmetric unit. |
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Components
#1: Protein | Mass: 27597.408 Da / Num. of mol.: 2 / Mutation: W154A, N-terminal Met added Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2M Ammonium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 21, 2005 |
Radiation | Monochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.4 Å / Num. all: 30362 / Num. obs: 30362 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 17.81 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 5.5 / Num. unique all: 4325 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 1K4F Resolution: 2.2→19.4 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.956 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.182 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.261 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→19.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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