+Open data
-Basic information
Entry | Database: PDB / ID: 4p62 | ||||||
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Title | Directed evolution of a B3 metallo-beta-lactamase AIM-1 | ||||||
Components | Metallo-beta-lactamase AIM-1 | ||||||
Keywords | HYDROLASE / Metallo-beta-lactamase / Antibiotic resistance / Directed evolution | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.89 Å | ||||||
Authors | Hou, C.-F.D. / Collyer, C. / Ollis, D.L. | ||||||
Citation | Journal: To Be Published Title: Directed evolution of a B3 metallo-beta-lactamase AIM-1 Authors: Hou, C.-F.D. / Collyer, C. / Ollis, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p62.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p62.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 4p62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4p62_validation.pdf.gz | 443.4 KB | Display | wwPDB validaton report |
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Full document | 4p62_full_validation.pdf.gz | 447 KB | Display | |
Data in XML | 4p62_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 4p62_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/4p62 ftp://data.pdbj.org/pub/pdb/validation_reports/p6/4p62 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31146.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaAIM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: B5DCA0 | ||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.09 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 8000, Zinc acetate, Sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.89 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.89 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→44.49 Å / Num. obs: 34233 / % possible obs: 99.8 % / Redundancy: 11 % / Net I/σ(I): 2.25 |
-Processing
Software |
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Refinement | Resolution: 1.89→66.21 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.032 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.101 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.199 Å2
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Refinement step | Cycle: 1 / Resolution: 1.89→66.21 Å
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Refine LS restraints |
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