+Open data
-Basic information
Entry | Database: PDB / ID: 8pgx | ||||||
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Title | Crystal structure of the metallo-beta-lactamase VIM1 with 3461 | ||||||
Components | Beta-lactamase VIM-1 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / Complex / metallo-beta-lactamase / inhibitor / zinc / indole carboxylate | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Calvopina, K. / Brem, J. / Farley, A.J.M. / Allen, M.D. / Schofield, C.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the metallo-beta-lactamase VIM1 with 3461 Authors: Calvopina, K. / Brem, J. / Farley, A.J.M. / Allen, M.D. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pgx.cif.gz | 199.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pgx.ent.gz | 133 KB | Display | PDB format |
PDBx/mmJSON format | 8pgx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pgx_validation.pdf.gz | 771.6 KB | Display | wwPDB validaton report |
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Full document | 8pgx_full_validation.pdf.gz | 775.8 KB | Display | |
Data in XML | 8pgx_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 8pgx_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/8pgx ftp://data.pdbj.org/pub/pdb/validation_reports/pg/8pgx | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28051.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM, blaVIM-1, CAZ10_38240, CAZ10_38245 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9XAY4 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-YKO / | Mass: 454.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23FN4O5 / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.2M ammonium phosphate 0.1M TrisHCl, pH 8.5 / PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→40.27 Å / Num. obs: 65566 / % possible obs: 99 % / Redundancy: 6.1 % / Biso Wilson estimate: 10.56 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.112 / Rsym value: 0.044 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.2→1.23 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4547 / CC1/2: 0.797 / Rpim(I) all: 0.266 / Rrim(I) all: 0.533 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→40.27 Å / SU ML: 0.0874 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.1503 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→40.27 Å
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Refine LS restraints |
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LS refinement shell |
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