antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function
Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details
THE AUTHOR SUGGESTS THE IDENTITY OF THE UNX ION IS SULPHUR
Sequence details
AUTHOR DEFINED DISCONTINUOUS RESIDUE NUMBERING. THE SEQUENCE IS NUMBERED ACCORDING TO THE BBL ...AUTHOR DEFINED DISCONTINUOUS RESIDUE NUMBERING. THE SEQUENCE IS NUMBERED ACCORDING TO THE BBL NUMBERING SCHEME (REFERENCE GARAU, G. ET AL (2004). UPDATE OF THE STANDARD NUMBERING SCHEME FOR CLASS B B -LACTAMASES. ANTIMICROB. AGENTS CHEMOTHER. 48, 2347-9.) HENCE GIVING INCONSECUTIVE NUMBERING OF RESIDUES.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 1.97 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal grow
pH: 5 Details: 22.5-23.5% POLYETHYLENE GLYCOL MONOMETHYL ETHERS (PEG MME) 2K, 0.1 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 5.0, 8 MM BETA-MERCAPTOETHANOL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.24 Å / Relative weight: 1
Reflection
Resolution: 2.33→50 Å / Num. obs: 10017 / % possible obs: 99.8 % / Observed criterion σ(I): 8.1 / Redundancy: 4.5 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.1
Reflection shell
Resolution: 2.33→2.46 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5
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Processing
Software
Name
Version
Classification
REFMAC
5.5.0102
refinement
XDS
datareduction
XDS
datascaling
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 2.33→25 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.882 / SU B: 7.494 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.428 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25405
1000
10 %
RANDOM
Rwork
0.18673
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obs
0.19338
8997
99.73 %
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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