+Open data
-Basic information
Entry | Database: PDB / ID: 3gvb | ||||||
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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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 3gvb.cif.gz | 168.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gvb.ent.gz | 133.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gvb_validation.pdf.gz | 473.6 KB | Display | wwPDB validaton report |
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Full document | 3gvb_full_validation.pdf.gz | 479.8 KB | Display | |
Data in XML | 3gvb_validation.xml.gz | 35 KB | Display | |
Data in CIF | 3gvb_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/3gvb ftp://data.pdbj.org/pub/pdb/validation_reports/gv/3gvb | HTTPS FTP |
-Related structure data
Related structure data | 3gqzC 3gr2C 3grjC 3gsgC 3gtcC 3gv9C 1ke4S C: citing same article (ref.) S: Starting model for refinement |
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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 | ChemComp-PO4 / #3: Chemical | ChemComp-3GV / ( | #4: Chemical | ChemComp-DMS / #5: 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: 2.48 Å3/Da / Density % sol: 50.39 % |
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Crystal grow | Temperature: 294 K / pH: 8.7 Details: 1.7M potassium phosphate, 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: 1.1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 25, 2008 |
Radiation | Protocol: SINGLE WAVELEGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→61.8 Å / Num. obs: 58911 / Redundancy: 3 % / Rmerge(I) obs: 0.073 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1KE4 Resolution: 1.8→58.12 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.299 / SU ML: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→58.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å
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