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Yorodumi- PDB-1xgj: AmpC beta-lactamase in complex with 3-(4-carboxy-2-hydroxy-phenyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xgj | ||||||
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Title | AmpC beta-lactamase in complex with 3-(4-carboxy-2-hydroxy-phenylsulfamoyl)-thiophene-2-carboxylic acid | ||||||
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: 1.97 Å | ||||||
Authors | Tondi, D. / Morandi, F. / Bonnet, R. / Costi, M.P. / Shoichet, B.K. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2005 Title: Structure-based optimization of a non-beta-lactam lead results in inhibitors that do not up-regulate beta-lactamase expression in cell culture. Authors: Tondi, D. / Morandi, F. / Bonnet, R. / Costi, M.P. / 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 | 1xgj.cif.gz | 160.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xgj.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 1xgj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/1xgj ftp://data.pdbj.org/pub/pdb/validation_reports/xg/1xgj | HTTPS FTP |
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-Related structure data
Related structure data | 1xgiC 1ke4S 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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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, ampA / Plasmid: POGO295 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / 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: 2.5 Å3/Da / Density % sol: 50.76 % |
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Crystal grow | Temperature: 294 K / pH: 8.7 Details: potassium phosphate buffer, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 8.70 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 23, 2004 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→20 Å / Num. obs: 51854 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 4.14 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.43 |
Reflection shell | Resolution: 1.97→2.04 Å / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 2.14 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KE4 Resolution: 1.97→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.97→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.04 Å / Total num. of bins used: 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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