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Yorodumi- PDB-2i72: AmpC beta-lactamase in complex with 5-diformylaminomethyl-benzo[b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i72 | ||||||
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Title | AmpC beta-lactamase in complex with 5-diformylaminomethyl-benzo[b]thiophen-2-boronic 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: 2.2 Å | ||||||
Authors | Venturelli, A. / Cancian, L. / Tondi, D. / Morandi, F. / Cannazza, G. / Segatore, B. / Prati, F. / Amicosante, G. / Shoichet, B.K. / Costi, M.P. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2007 Title: Optimizing Cell Permeation of an Antibiotic Resistance Inhibitor for Improved Efficacy Authors: Venturelli, A. / Tondi, D. / Cancian, L. / Morandi, F. / Cannazza, G. / Segatore, B. / Prati, F. / Amicosante, G. / Shoichet, B.K. / Costi, M.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i72.cif.gz | 156.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i72.ent.gz | 122.5 KB | Display | PDB format |
PDBx/mmJSON format | 2i72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i72_validation.pdf.gz | 964.9 KB | Display | wwPDB validaton report |
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Full document | 2i72_full_validation.pdf.gz | 961.4 KB | Display | |
Data in XML | 2i72_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 2i72_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/2i72 ftp://data.pdbj.org/pub/pdb/validation_reports/i7/2i72 | HTTPS FTP |
-Related structure data
Related structure data | 1cb3S 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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Unit cell |
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-Components
#1: Protein | Mass: 39587.922 Da / Num. of mol.: 2 / Fragment: Residues 20-377 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 | #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: 50.89 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: potassium phosphate buffer, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 18, 2004 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115869 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→45.314 Å / Num. obs: 39060 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 3.9 / Num. measured all: 20830 / Num. unique all: 5590 / Rsym value: 0.345 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CB3 Resolution: 2.2→45.31 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.492 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.19 / 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: 20.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→45.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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