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Yorodumi- PDB-4pvo: Crystal Structure of VIM-2 metallo-beta-lactamase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pvo | ||||||
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Title | Crystal Structure of VIM-2 metallo-beta-lactamase in complex with ML302 and ML302F | ||||||
Components | Beta-lactamase class B VIM-2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / alpha-beta/beta-alpha fold / beta-lactamase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / molecular replacement / Resolution: 1.48 Å | ||||||
Authors | Aik, W.S. / Brem, J. / McDonough, M.A. / Schofield, C.J. | ||||||
Citation | Journal: Nat.Chem. / Year: 2014 Title: Rhodanine hydrolysis leads to potent thioenolate mediated metallo-beta-lactamase inhibition. Authors: Brem, J. / van Berkel, S.S. / Aik, W. / Rydzik, A.M. / Avison, M.B. / Pettinati, I. / Umland, K.D. / Kawamura, A. / Spencer, J. / Claridge, T.D. / McDonough, M.A. / 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 | 4pvo.cif.gz | 201.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pvo.ent.gz | 158.6 KB | Display | PDB format |
PDBx/mmJSON format | 4pvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pvo_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4pvo_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4pvo_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 4pvo_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/4pvo ftp://data.pdbj.org/pub/pdb/validation_reports/pv/4pvo | HTTPS FTP |
-Related structure data
Related structure data | 4pvtC 4tytC 1ko3S 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25693.488 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-266 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla-VIM-2, blasVIM-2, blaVIM-2, blaVIM2, VIM-2 / Plasmid: pOPIN-F VIM-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K2N0 |
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-Non-polymers , 6 types, 550 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-SVB / | #5: Chemical | ChemComp-FMT / #6: Chemical | ChemComp-DMS / | #7: Water | ChemComp-HOH / | |
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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: 2.05 Å3/Da / Density % sol: 39.99 % / Mosaicity: 0.2 ° / Mosaicity esd: 0.004 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1mM TCEP, 2.5mM ML302, 50mM HEPES pH 7.5, 100mM NaCl, 0.1mM ZnCl2, 0.1M magnesium formate, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.8344 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2013 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8344 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.48→50 Å / Num. all: 68860 / Num. obs: 68140 / % possible obs: 98.954 % / Observed criterion σ(F): -3 / Redundancy: 5 % / Biso Wilson estimate: 10.65 Å2 / Rmerge(I) obs: 0.136 / Χ2: 1.202 / Net I/σ(I): 13 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1KO3 Resolution: 1.48→39.1 Å / Isotropic thermal model: isotropic
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Displacement parameters | Biso max: 70.96 Å2 / Biso mean: 17.7609 Å2 / Biso min: 5.05 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→39.1 Å
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Refine LS restraints |
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LS refinement shell |
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