+Open data
-Basic information
Entry | Database: PDB / ID: 1ke4 | ||||||
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Title | X-ray crystal structure of AmpC beta-lactamase from E. coli | ||||||
Components | beta-lactamase | ||||||
Keywords | HYDROLASE / cephalosporinase / beta-lactamase / serine hydrolase | ||||||
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: 1.72 Å | ||||||
Authors | Powers, R.A. / Shoichet, B.K. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2002 Title: Structure-based approach for binding site identification on AmpC beta-lactamase. Authors: Powers, R.A. / 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 | 1ke4.cif.gz | 152.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ke4.ent.gz | 119.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ke4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/1ke4 ftp://data.pdbj.org/pub/pdb/validation_reports/ke/1ke4 | HTTPS FTP |
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-Related structure data
Related structure data | 1kdsC 1kdwC 1ke0C 1ke3C 2blsS 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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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: 51.35 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.7 M potassium phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / Details: used microseeding | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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: Jan 22, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→20 Å / Num. all: 83561 / Num. obs: 81989 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 23.87 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.72→1.76 Å / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 5.1 / % possible all: 97.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 322742 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 97.8 % / Rmerge(I) obs: 0.372 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2BLS Resolution: 1.72→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: Residues 285-290 of chain A were not seen in the electron density.
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.72→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.8 Å
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.214 / Rfactor Rwork: 0.19 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.2305 / % reflection Rfree: 4 % / Rfactor Rwork: 0.2002 |