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- PDB-3b3x: Crystal structure of class A beta-lactamase of Bacillus lichenifo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3b3x | ||||||
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Title | Crystal structure of class A beta-lactamase of Bacillus licheniformis BS3 with aminocitrate | ||||||
![]() | Beta-lactamase![]() | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / ![]() ![]() | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sauvage, E. / Herman, R. / Kerff, F. / Charlier, P. | ||||||
![]() | ![]() Title: 2-Aminopropane-1,2,3-tricarboxylic acid: Synthesis and co-crystallization with the class A beta-lactamase BS3 of Bacillus licheniformis Authors: Beck, J. / Sauvage, E. / Charlier, P. / Marchand-Brynaert, 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 | ![]() | 113.7 KB | Display | ![]() |
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PDB format | ![]() | 88.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1w7fS S: Starting model for refinement |
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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: 29513.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: P94458, UniProt: P00808*PLUS, ![]() #2: Chemical | #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.37 % |
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Crystal grow![]() | Temperature: 293 K / Method: hanging drop / pH: 7.2 Details: 5micro-l of a protein solution (at a concentration of 38mg/ml in 50mM NaCl, 10mM Tris buffer, pH 7.2), 4micro-l of 8% PEG 6000 in 100mM sodium aminocitrate buffer (pH 3.4) plus 1micro-l of 0. ...Details: 5micro-l of a protein solution (at a concentration of 38mg/ml in 50mM NaCl, 10mM Tris buffer, pH 7.2), 4micro-l of 8% PEG 6000 in 100mM sodium aminocitrate buffer (pH 3.4) plus 1micro-l of 0.1M urea additive, equilibrated against 1ml of a 20% PEG 6000, 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: Mar 4, 2005 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→63.758 Å / Num. obs: 17440 / % possible obs: 82.3 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 7.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1W7F Resolution: 2.5→36.47 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.831 / SU B: 11.704 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.393 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.959 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→36.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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