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Yorodumi- PDB-6jed: Crystal structure of IMP-1 metallo-beta-lactamase in a complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jed | |||||||||
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Title | Crystal structure of IMP-1 metallo-beta-lactamase in a complex with MCR | |||||||||
Components | Metallo-beta-lactamase type 2 | |||||||||
Keywords | HYDROLASE / metallo-beta-lactamase | |||||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | |||||||||
Biological species | Serratia marcescens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | |||||||||
Authors | Wachino, J. | |||||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2019 Title: 4-Amino-2-Sulfanylbenzoic Acid as a Potent Subclass B3 Metallo-beta-Lactamase-Specific Inhibitor Applicable for Distinguishing Metallo-beta-Lactamase Subclasses. Authors: Wachino, J. / Kanechi, R. / Nishino, E. / Mochizuki, M. / Jin, W. / Kimura, K. / Kurosaki, H. / Arakawa, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jed.cif.gz | 65 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jed.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 6jed.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/6jed ftp://data.pdbj.org/pub/pdb/validation_reports/je/6jed | HTTPS FTP |
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-Related structure data
Related structure data | 5y5bSC 6k4tC 6k4xC 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: 25146.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P52699, beta-lactamase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MCR / | #4: Chemical | ChemComp-EPE / | #5: 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: 2.05 Å3/Da / Density % sol: 40.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium acetate, 0.1M sodium HEPES buffer (pH 7.5), 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: AR-NW12A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→56.82 Å / Num. obs: 29943 / % possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.57→1.65 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 6.4 / Num. unique obs: 4256 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y5B Resolution: 1.57→50.53 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.446 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.084 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.085 Å2
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Refinement step | Cycle: 1 / Resolution: 1.57→50.53 Å
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Refine LS restraints |
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