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Yorodumi- PDB-5n5i: Crystal Structure of VIM-1 metallo-beta-lactamase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n5i | ||||||
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Title | Crystal Structure of VIM-1 metallo-beta-lactamase in complex with hydrolysed meropenem | ||||||
Components | Beta-lactamase VIM-1 | ||||||
Keywords | HYDROLASE / lactamase / carbapenemase / antibiotic / meropenem | ||||||
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: 2.2 Å | ||||||
Authors | Salimraj, R. / Hinchliffe, P. / Spencer, J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: FEBS J. / Year: 2019 Title: Crystal structures of VIM-1 complexes explain active site heterogeneity in VIM-class metallo-beta-lactamases. Authors: Salimraj, R. / Hinchliffe, P. / Kosmopoulou, M. / Tyrrell, J.M. / Brem, J. / van Berkel, S.S. / Verma, A. / Owens, R.J. / McDonough, M.A. / Walsh, T.R. / Schofield, C.J. / Spencer, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n5i.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n5i.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 5n5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n5i_validation.pdf.gz | 735.2 KB | Display | wwPDB validaton report |
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Full document | 5n5i_full_validation.pdf.gz | 735.9 KB | Display | |
Data in XML | 5n5i_validation.xml.gz | 12 KB | Display | |
Data in CIF | 5n5i_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/5n5i ftp://data.pdbj.org/pub/pdb/validation_reports/n5/5n5i | HTTPS FTP |
-Related structure data
Related structure data | 5n5gSC 5n5hC S: Starting model for refinement C: citing same article (ref.) |
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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: 26898.760 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaVIM, blaVIM-1 / Plasmid: pOPIN-E / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q9XAY4 | ||||
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#2: Chemical | #3: Chemical | ChemComp-LMP / ( | #4: 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: 2.03 Å3/Da / Density % sol: 39.55 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.03 M MgCl2, 0.03 M CaCl2, 0.1 M MOPS pH 7.5, 0.1 M HEPES sodium salt pH 7.50, 12.5% w/v PEG 3350, 12.5% w/v PEG 1000, 12.5% w/v MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→27.841 Å / Num. obs: 10547 / % possible obs: 99.2 % / Redundancy: 5.8 % / CC1/2: 0.988 / Rmerge(I) obs: 0.182 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 4.2 / CC1/2: 0.87 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N5G Resolution: 2.2→27.841 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→27.841 Å
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Refine LS restraints |
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LS refinement shell |
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