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Yorodumi- PDB-1my8: AmpC beta-lactamase in complex with an M.carboxyphenylglycylboron... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1my8 | ||||||
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Title | AmpC beta-lactamase in complex with an M.carboxyphenylglycylboronic acid bearing the cephalothin R1 side chain | ||||||
Components | beta-lactamase | ||||||
Keywords | HYDROLASE / AmpC / beta-lactamase / cephalosporinase / 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 | Morandi, F. / Caselli, E. / Morandi, S. / Focia, P.J. / Blazquez, J. / Shoichet, B.K. / Prati, F. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2003 Title: Nanomolar inhibitors of AmpC beta-lactamase. Authors: Morandi, F. / Caselli, E. / Morandi, S. / Focia, P.J. / Blazquez, J. / Shoichet, B.K. / Prati, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1my8.cif.gz | 158.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1my8.ent.gz | 131.2 KB | Display | PDB format |
PDBx/mmJSON format | 1my8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/1my8 ftp://data.pdbj.org/pub/pdb/validation_reports/my/1my8 | HTTPS FTP |
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-Related structure data
Related structure data | 1mxoC 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) / Gene: ampc / Plasmid: POGO295 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / 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: 2.27 Å3/Da / Density % sol: 45.28 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: potassium phosphate buffer, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||
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: Jun 12, 2002 |
Radiation | Monochromator: mirrors / 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: 82999 / Num. obs: 82138 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.27 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 29.99 |
Reflection shell | Resolution: 1.72→1.76 Å / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 11.23 / % possible all: 96 |
Reflection | *PLUS % possible obs: 99.2 % / Num. measured all: 350811 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 96 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 11.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FSY Resolution: 1.72→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.72→20 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.189 / Rfactor Rwork: 0.167 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.72 Å / Lowest resolution: 1.76 Å |