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Yorodumi- PDB-1iem: Crystal Structure of AmpC beta-lactamase from E. coli in Complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iem | ||||||
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Title | Crystal Structure of AmpC beta-lactamase from E. coli in Complex with a Boronic Acid Inhibitor (1, CefB4) | ||||||
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: 2.3 Å | ||||||
Authors | Powers, R.A. / Caselli, E. / Focia, P.J. / Prati, F. / Shoichet, B.K. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Structures of ceftazidime and its transition-state analogue in complex with AmpC beta-lactamase: implications for resistance mutations and inhibitor design. Authors: Powers, R.A. / Caselli, E. / Focia, P.J. / Prati, F. / 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 | 1iem.cif.gz | 152.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iem.ent.gz | 120.2 KB | Display | PDB format |
PDBx/mmJSON format | 1iem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iem_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1iem_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1iem_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 1iem_validation.cif.gz | 40.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/1iem ftp://data.pdbj.org/pub/pdb/validation_reports/ie/1iem | HTTPS FTP |
-Related structure data
Related structure data | 1ielC 1fsyS 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) / Plasmid: p0G0295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase #2: Chemical | ChemComp-PO4 / | #3: Chemical | #4: 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: 2.56 Å3/Da / Density % sol: 52.03 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.7M potassium phosphate, 95uM AmpC, 586uM compound 1 (CB4), 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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 4, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 35024 / Num. obs: 137203 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 26.68 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.359 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 35024 / Num. measured all: 137203 |
Reflection shell | *PLUS % possible obs: 99.9 % / Mean I/σ(I) obs: 4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1FSY Resolution: 2.3→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 6 % / Rfactor obs: 0.182 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.217 |