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Yorodumi- PDB-6lbl: Crystal structure of IMP-1 metallo-beta-lactamase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lbl | ||||||
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Title | Crystal structure of IMP-1 metallo-beta-lactamase in complex with NO9 inhibitor | ||||||
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: 1.68 Å | ||||||
Authors | Wachino, J. | ||||||
Citation | Journal: Mbio / Year: 2020 Title: Sulfamoyl Heteroarylcarboxylic Acids as Promising Metallo-beta-Lactamase Inhibitors for Controlling Bacterial Carbapenem Resistance. Authors: Wachino, J.I. / Jin, W. / Kimura, K. / Kurosaki, H. / Sato, A. / Arakawa, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lbl.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lbl.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 6lbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lbl_validation.pdf.gz | 925.4 KB | Display | wwPDB validaton report |
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Full document | 6lbl_full_validation.pdf.gz | 927 KB | Display | |
Data in XML | 6lbl_validation.xml.gz | 13 KB | Display | |
Data in CIF | 6lbl_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/6lbl ftp://data.pdbj.org/pub/pdb/validation_reports/lb/6lbl | HTTPS FTP |
-Related structure data
Related structure data | 6kxiC 6kxoC 6kzlC 6kznC 5ev6S 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-NA / | #4: Chemical | ChemComp-NO9 / | #5: 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: 2.03 Å3/Da / Density % sol: 39.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 3350, 0.2M sodium acetate, 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→56.61 Å / Num. obs: 24088 / % possible obs: 99.7 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.68→1.77 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.281 / Num. unique obs: 3462 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ev6 Resolution: 1.68→49.386 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.973 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.105 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→49.386 Å
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Refine LS restraints |
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LS refinement shell |
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