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Yorodumi- PDB-1ll5: X-ray crystal structure of AmpC WT beta-lactamase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ll5 | ||||||
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Title | X-ray crystal structure of AmpC WT beta-lactamase in complex with covalently bound imipenem | ||||||
Components | beta-lactamase | ||||||
Keywords | HYDROLASE / beta-lactamase / carbapenem / imipenem | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Beadle, B.M. / Shoichet, B.K. | ||||||
Citation | Journal: ANTIMICROB.AGENTS CHEMOTHER. / Year: 2002 Title: Structural Basis for Imipenem Inhibition of Class C beta-lactamases Authors: Beadle, B.M. / Shoichet, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ll5.cif.gz | 152.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ll5.ent.gz | 120.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ll5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/1ll5 ftp://data.pdbj.org/pub/pdb/validation_reports/ll/1ll5 | HTTPS FTP |
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-Related structure data
Related structure data | 1ke4S 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: 39587.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: K12 / Plasmid: pOGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase #2: Chemical | #3: 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: 2.53 Å3/Da / Density % sol: 51.36 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.7 M potassium phosphate; crystal was then soaked in saturated imipenem for 40 minutes, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal grow | *PLUS |
Components of the solutions | *PLUS Conc.: 1.7 M / Common name: potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 31, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 64997 / Num. obs: 64997 / % possible obs: 88.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 7.4 / % possible all: 96.4 |
Reflection | *PLUS Num. measured all: 230232 |
Reflection shell | *PLUS % possible obs: 96.4 % / Mean I/σ(I) obs: 7.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1KE4 Resolution: 1.8→20 Å / σ(F): 2 Details: Residues 284-290 of chain A were not seen in the electron density.
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Solvent computation | Bsol: 0.382851 Å2 / ksol: 45.6696 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 4 % | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.015 |