+Open data
-Basic information
Entry | Database: PDB / ID: 2uyx | |||||||||
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Title | metallo-beta-lactamase (1BC2) single point mutant D120S | |||||||||
Components | BETA-LACTAMASE II | |||||||||
Keywords | HYDROLASE / PENICILLINASE / METAL-BINDING / ANTIBIOTIC RESISTANCE / METALLO BETA- LACTAMASE | |||||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | |||||||||
Biological species | BACILLUS CEREUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Larrull, L.I. / Fabiane, S.M. / Kowalski, J.M. / Bennett, B. / Sutton, B.J. / Vila, A.J. | |||||||||
Citation | Journal: J. Biol. Chem. / Year: 2007 Title: Asp-120 locates Zn2 for optimal metallo-beta-lactamase activity. Authors: Llarrull, L.I. / Fabiane, S.M. / Kowalski, J.M. / Bennett, B. / Sutton, B.J. / Vila, A.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uyx.cif.gz | 66.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uyx.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 2uyx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/2uyx ftp://data.pdbj.org/pub/pdb/validation_reports/uy/2uyx | HTTPS FTP |
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-Related structure data
Related structure data | 3bc2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25038.602 Da / Num. of mol.: 1 / Fragment: RESIDUES 30-257 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Strain: 569/H/9 / Cell line (production host): JM109 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P04190, beta-lactamase | ||||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | N-TERMINUS DISORDERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 19% PEG 3350, 0.1M NA CACODYLATE PH 5.5, 0.1M NA TARTRATE, 25% GLYCEROL ADDED AS CRYOPROTECTANT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.985 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 23, 2004 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.985 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→31.01 Å / Num. obs: 16580 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BC2 Resolution: 1.95→31.01 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.272 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N-TERMINUS AND RESIDUES 61-65 DISORDERED
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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: 27.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→31.01 Å
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Refine LS restraints |
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