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Yorodumi- PDB-4c1h: Crystal structure of the metallo-beta-lactamase BCII with L-captopril -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c1h | ||||||
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Title | Crystal structure of the metallo-beta-lactamase BCII with L-captopril | ||||||
Components | BETA-LACTAMASE 2 | ||||||
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 | BACILLUS CEREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 | 4c1h.cif.gz | 122.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c1h.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 4c1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c1h_validation.pdf.gz | 463.3 KB | Display | wwPDB validaton report |
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Full document | 4c1h_full_validation.pdf.gz | 464.1 KB | Display | |
Data in XML | 4c1h_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 4c1h_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/4c1h ftp://data.pdbj.org/pub/pdb/validation_reports/c1/4c1h | HTTPS FTP |
-Related structure data
Related structure data | 4bz3C 4c09C 4c1cC 4c1dC 4c1eC 4c1fC 4c1gC 1mqoS 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24995.533 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-257 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Strain: 569/H/9 / Description: CHROMOSOME DERIVED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P04190, beta-lactamase |
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-Non-polymers , 5 types, 299 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-X8Z / | #5: Chemical | #6: 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: 5.5 Details: 0.2 M AMMONIUM SULFATE, 0.1 M BIS TRIS, 25 % W/V PEG 3350, PH 5.5, 1 MM TCEP. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 22, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. obs: 89049 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 12.06 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.05 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.97 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MQO Resolution: 1.1→40.074 Å / SU ML: 0.07 / σ(F): 1.36 / Phase error: 12.42 / Stereochemistry target values: ML Details: CONFORMATION OF RAMACHANDRAN OUTLIERS 86 ASP, 87 SER AND 245 ASP VALIDATED BY CLEAR ELECTRON DENSITY. RAMACHANDRAN OUTLIERS 117 ALA AND 234 ASN VALIDATED BY ELECTRON DENSITY AND ARE ...Details: CONFORMATION OF RAMACHANDRAN OUTLIERS 86 ASP, 87 SER AND 245 ASP VALIDATED BY CLEAR ELECTRON DENSITY. RAMACHANDRAN OUTLIERS 117 ALA AND 234 ASN VALIDATED BY ELECTRON DENSITY AND ARE CONSISTENT WITH CONFORMATIONS IN PDB ENTRY 4C09. POSSIBLE OXIDISED CYS 198 AT VERY LOW OCCUPANCY LEFT UNMODELED DUE TO LOW OCCUPANCY. RESIDUES 41-44 AND 63-67 ARE DISORDERED.
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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: 18.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→40.074 Å
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Refine LS restraints |
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LS refinement shell |
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