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Yorodumi- PDB-4c1f: Crystal structure of the metallo-beta-lactamase IMP-1 with L-captopril -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c1f | ||||||
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Title | Crystal structure of the metallo-beta-lactamase IMP-1 with L-captopril | ||||||
Components | BETA-LACTAMASE IMP-1 | ||||||
Keywords | HYDROLASE / MBL / METALLO-BETA-LACTAMASE / ANTIBIOTIC RESISTANCE | ||||||
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: 2.01 Å | ||||||
Authors | Zollman, D. / Brem, J. / McDonough, M.A. / van Berkel, S.S. / Schofield, C.J. | ||||||
Citation | Journal: Antimicrob. Agents Chemother. / Year: 2015 Title: Structural Basis of Metallo-beta-Lactamase Inhibition by Captopril Stereoisomers. Authors: Brem, J. / van Berkel, S.S. / Zollman, D. / Lee, S.Y. / Gileadi, O. / McHugh, P.J. / Walsh, T.R. / 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 | 4c1f.cif.gz | 186.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c1f.ent.gz | 147.5 KB | Display | PDB format |
PDBx/mmJSON format | 4c1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/4c1f ftp://data.pdbj.org/pub/pdb/validation_reports/c1/4c1f | HTTPS FTP |
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-Related structure data
Related structure data | 4bz3C 4c09C 4c1cC 4c1dC 4c1eC 4c1gC 4c1hC 1dd6S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 25146.676 Da / Num. of mol.: 2 / Fragment: RESIDUES 19-245 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Description: PLASMID DERIVED NON-GENOMIC. / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P52699, beta-lactamase #2: Chemical | ChemComp-X8Z / | #3: Chemical | #4: Chemical | ChemComp-ZN / #5: 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 4.5 Details: 0.05 M LI2SO4, 0.1 M SODIUM ACETATE, PH 4.5, 23 % W/V PEG 8000, 1MM DTT. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9626 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: May 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9626 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→52.5 Å / Num. obs: 36158 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 27.43 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.01→2.08 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.8 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DD6 Resolution: 2.01→52.568 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 21.05 / Stereochemistry target values: ML Details: CHAIN B IS MORE DISORDERED THAN CHAIN A AS INDICATED BY THE AVERAGE B-FACTORS - CHAIN A 22.3 VS CHAIN B 70.7. CONFORMATION OF RAMACHANDRAN OUTLIERS 59 ASN AND 66 ASP VALIDATED BY CLEAR ...Details: CHAIN B IS MORE DISORDERED THAN CHAIN A AS INDICATED BY THE AVERAGE B-FACTORS - CHAIN A 22.3 VS CHAIN B 70.7. CONFORMATION OF RAMACHANDRAN OUTLIERS 59 ASN AND 66 ASP VALIDATED BY CLEAR ELECTRON DENSITY IN CHAIN A.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→52.568 Å
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Refine LS restraints |
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LS refinement shell |
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