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Yorodumi- PDB-5aeb: Crystal structure of the class B3 di-zinc metallo-beta-lactamase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aeb | ||||||
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Title | Crystal structure of the class B3 di-zinc metallo-beta-lactamase LRA- 12 from an Alaskan soil metagenome. | ||||||
Components | LRA-12 | ||||||
Keywords | HYDROLASE / MBL / CARBAPENEMASE / METAGENOMICS / CARBAPENEM-RESISTANCE / ENVIRONMENTAL RESISTOME | ||||||
Function / homology | Function and homology information | ||||||
Biological species | UNCULTURED BACTERIUM BLR12 (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Power, P. / Herman, R. / Kerff, F. / Bouillenne, F. / Rodriguez, M.M. / Galleni, M. / Handelsman, J. / Gutkind, G. / Charlier, P. / Sauvage, E. | ||||||
Citation | Journal: PLoS ONE / Year: 2017 Title: Crystal structure and kinetic analysis of the class B3 di-zinc metallo-beta-lactamase LRA-12 from an Alaskan soil metagenome. Authors: Rodriguez, M.M. / Herman, R. / Ghiglione, B. / Kerff, F. / D'Amico Gonzalez, G. / Bouillenne, F. / Galleni, M. / Handelsman, J. / Charlier, P. / Gutkind, G. / Sauvage, E. / Power, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aeb.cif.gz | 220.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aeb.ent.gz | 178.1 KB | Display | PDB format |
PDBx/mmJSON format | 5aeb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/5aeb ftp://data.pdbj.org/pub/pdb/validation_reports/ae/5aeb | HTTPS FTP |
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-Related structure data
Related structure data | 1jt1S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30410.639 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26-293 / Source method: isolated from a natural source Details: METAGENOMIC-DERIVED BETA-LACTAMASE FROM ALASKAN SOIL Source: (natural) UNCULTURED BACTERIUM BLR12 (environmental samples) References: UniProt: B5L5V5, beta-lactamase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CO / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 47.8 % / Description: NONE |
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Crystal grow | Details: 25% PEG 3350, 0.1M TRIS (PH 8.5), 0.2 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.59 Å / Num. obs: 33531 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.3 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JT1 Resolution: 2.1→42.93 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.904 / SU B: 7.897 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
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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: 26.509 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→42.93 Å
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Refine LS restraints |
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