+Open data
-Basic information
Entry | Database: PDB / ID: 3grj | ||||||
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Title | AmpC beta-lactamase in complex with Fragment-based Inhibitor | ||||||
Components | Beta-lactamase | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Antibiotic resistance / Hydrolase / 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 / molecular replacement / Resolution: 2.49 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 | 3grj.cif.gz | 160.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3grj.ent.gz | 127 KB | Display | PDB format |
PDBx/mmJSON format | 3grj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3grj_validation.pdf.gz | 490.6 KB | Display | wwPDB validaton report |
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Full document | 3grj_full_validation.pdf.gz | 501.6 KB | Display | |
Data in XML | 3grj_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | 3grj_validation.cif.gz | 44 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/3grj ftp://data.pdbj.org/pub/pdb/validation_reports/gr/3grj | HTTPS FTP |
-Related structure data
Related structure data | 3gqzC 3gr2C 3gsgC 3gtcC 3gv9C 3gvbC 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
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 260 molecules
#2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 50.72 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 400 mM KPi at pH 8.5 with 25% PEG 3350, at 294K, VAPOR DIFFUSION, HANGING DROP |
-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: Jun 21, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 30971 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.133 / Χ2: 3.488 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1KE4 Resolution: 2.49→45.27 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 11.017 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.005 / ESU R Free: 0.311 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.5 Å2 / Biso mean: 41.99 Å2 / Biso min: 26.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→45.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.49→2.552 Å / Total num. of bins used: 20
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