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Yorodumi- PDB-8i52: Crystal structure of VIM-2 metallo-beta-lactamase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i52 | ||||||
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Title | Crystal structure of VIM-2 metallo-beta-lactamase in complex with 10-HHIA | ||||||
Components | Beta-lactamase class B VIM-2 | ||||||
Keywords | HYDROLASE / beta-lactamase | ||||||
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: 1.58 Å | ||||||
Authors | Wachino, J. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of VIM-2 Metallo-beta-lactamase in complex with 10-HHIA Authors: Wachino, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i52.cif.gz | 121.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i52.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 8i52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i52_validation.pdf.gz | 765.6 KB | Display | wwPDB validaton report |
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Full document | 8i52_full_validation.pdf.gz | 766.3 KB | Display | |
Data in XML | 8i52_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 8i52_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/8i52 ftp://data.pdbj.org/pub/pdb/validation_reports/i5/8i52 | HTTPS FTP |
-Related structure data
Related structure data | 5yd7S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26142.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255 Production host: Escherichia coli (E. coli) / References: UniProt: Q9K2N0, beta-lactamase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-OR6 / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-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: 41.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Magnesium formate dehydrate, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→55.393 Å / Num. obs: 55926 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.034 / Rrim(I) all: 0.089 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.58→1.67 Å / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 8 / Num. unique obs: 8043 / Rpim(I) all: 0.084 / Rrim(I) all: 0.221 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YD7 Resolution: 1.58→55.393 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.156 / SU B: 1.316 / SU ML: 0.048 / Average fsc free: 0.9795 / Average fsc work: 0.9864 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.081 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.261 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→55.393 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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