+Open data
-Basic information
Entry | Database: PDB / ID: 3gtc | ||||||
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Title | AmpC beta-lactamase in complex with Fragment-based Inhibitor | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Hydrolase / Antibiotic resistance / Periplasm / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Teotico, D.T. / Shoichet, B.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Docking for fragment inhibitors of AmpC beta-lactamase Authors: Teotico, D.G. / Babaoglu, K. / Rocklin, G.J. / Ferreira, R.S. / Giannetti, A.M. / 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 | 3gtc.cif.gz | 165.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gtc.ent.gz | 131.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gtc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gtc_validation.pdf.gz | 462.1 KB | Display | wwPDB validaton report |
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Full document | 3gtc_full_validation.pdf.gz | 471.6 KB | Display | |
Data in XML | 3gtc_validation.xml.gz | 35.4 KB | Display | |
Data in CIF | 3gtc_validation.cif.gz | 53.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/3gtc ftp://data.pdbj.org/pub/pdb/validation_reports/gt/3gtc | HTTPS FTP |
-Related structure data
Related structure data | 3gqzC 3gr2C 3grjC 3gsgC 3gv9C 3gvbC 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) / Strain: K12 / Gene: ampA, ampC, b4150, JW4111 / Plasmid: pOGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase #2: Chemical | #3: Chemical | ChemComp-GTC / ( #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: 2.57 Å3/Da / Density % sol: 52.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.7M potassium phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 18, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 62779 / % possible obs: 98.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.063 / Χ2: 1.325 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.18 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.847 / SU B: 4.176 / SU ML: 0.121 / SU R Cruickshank DPI: 0.432 / SU Rfree: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.157 / 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 max: 72.08 Å2 / Biso mean: 25.94 Å2 / Biso min: 10.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.946 Å / Total num. of bins used: 20
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