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Yorodumi- PDB-2rcx: AmpC Beta-lactamase in complex with (1R)-1-(2-Thiophen-2-yl-acety... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rcx | ||||||
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Title | AmpC Beta-lactamase in complex with (1R)-1-(2-Thiophen-2-yl-acetylamino)-1-(3-(2-carboxyvinyl)-phenyl) methylboronic acid | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / AmpC / beta-lactamase / cephalosporinase / serine hydrolase / Antibiotic resistance / Periplasm | ||||||
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 Å | ||||||
Authors | Morandi, F. / Morandi, S. / Prati, F. / Shoichet, B.K. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2008 Title: Structure-based optimization of cephalothin-analogue boronic acids as beta-lactamase inhibitors Authors: Morandi, S. / Morandi, F. / Caselli, E. / 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 | 2rcx.cif.gz | 161.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rcx.ent.gz | 126.9 KB | Display | PDB format |
PDBx/mmJSON format | 2rcx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/2rcx ftp://data.pdbj.org/pub/pdb/validation_reports/rc/2rcx | 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: 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: 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: 2.52 Å3/Da / Density % sol: 51.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: potassium phosphate buffer, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115889 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 18, 2005 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115889 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 53511 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.069 / Χ2: 0.91 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.07 / Num. unique all: 5302 / Χ2: 0.683 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1KE4 Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.777 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.927 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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