+Open data
-Basic information
Entry | Database: PDB / ID: 8pgk | ||||||
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Title | Crystal structure of the metallo-beta-lactamase VIM1 with 3016 | ||||||
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: 1.24 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 3016 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 | 8pgk.cif.gz | 192.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pgk.ent.gz | 133.2 KB | Display | PDB format |
PDBx/mmJSON format | 8pgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pgk_validation.pdf.gz | 1015.3 KB | Display | wwPDB validaton report |
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Full document | 8pgk_full_validation.pdf.gz | 1023.3 KB | Display | |
Data in XML | 8pgk_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 8pgk_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/8pgk ftp://data.pdbj.org/pub/pdb/validation_reports/pg/8pgk | 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-YVH / | Mass: 543.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26FN5O6S / 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: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→34.08 Å / Num. obs: 57167 / % possible obs: 95.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 13.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.05 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.24→1.27 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3151 / CC1/2: 0.749 / Rpim(I) all: 0.311 / Rrim(I) all: 0.736 / % possible all: 71.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→29.14 Å / SU ML: 0.1059 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.7783 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: 18.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.24→29.14 Å
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Refine LS restraints |
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LS refinement shell |
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