+Open data
-Basic information
Entry | Database: PDB / ID: 2qz6 | ||||||
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Title | First crystal structure of a psychrophile class C beta-lactamase | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / class C beta-lactamase / psychrophile / cold adaptation / Antibiotic resistance / Periplasm | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / molecular replacement / Resolution: 2.26 Å | ||||||
Authors | Michaux, C. / Massant, J. / Kerff, F. / Charlier, P. / Wouters, J. | ||||||
Citation | Journal: Febs J. / Year: 2008 Title: Crystal structure of a cold-adapted class C beta-lactamase Authors: Michaux, C. / Massant, J. / Kerff, F. / Docquier, J.D. / Vandenberghe, I. / Samyn, B. / Pierrard, A. / Feller, G. / Charlier, P. / Van Beeumen, J. / Wouters, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qz6.cif.gz | 82.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qz6.ent.gz | 60.3 KB | Display | PDB format |
PDBx/mmJSON format | 2qz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qz6_validation.pdf.gz | 414.3 KB | Display | wwPDB validaton report |
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Full document | 2qz6_full_validation.pdf.gz | 427.1 KB | Display | |
Data in XML | 2qz6_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 2qz6_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/2qz6 ftp://data.pdbj.org/pub/pdb/validation_reports/qz/2qz6 | HTTPS FTP |
-Related structure data
Related structure data | 2blt 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: 38764.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas fluorescens (bacteria) / Strain: TAE 4 / References: UniProt: P85302, beta-lactamase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: 20% PEG 6K, 0.1M Tris, pH8.0, vapor diffusion, temperature 298K, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 2, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 15724 / % possible obs: 95.4 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.038 / Net I/σ(I): 23.94 |
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 16.62 / Num. unique all: 7667 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: AB INITIO Starting model: PDB ENTRY 2BLT 2blt Resolution: 2.26→19.12 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.873 / Num. parameters: 10919 / Num. restraintsaints: 11088 / SU B: 5.706 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.432 / ESU R Free: 0.253 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.568 Å2
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2715 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→19.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.26→2.318 Å / Total num. of bins used: 20
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