+Open data
-Basic information
Entry | Database: PDB / ID: 2r9x | ||||||
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Title | AmpC beta-lactamase with bound Phthalamide inhibitor | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / AmpC beta-lactamase / pthalamide / Antibiotic resistance | ||||||
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 | Babaoglu, K. / Shoichet, B.K. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase. Authors: Babaoglu, K. / Simeonov, A. / Irwin, J.J. / Nelson, M.E. / Feng, B. / Thomas, C.J. / Cancian, L. / Costi, M.P. / Maltby, D.A. / Jadhav, A. / Inglese, J. / Austin, C.P. / 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 | 2r9x.cif.gz | 173.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r9x.ent.gz | 137.5 KB | Display | PDB format |
PDBx/mmJSON format | 2r9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r9x_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2r9x_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2r9x_validation.xml.gz | 35.9 KB | Display | |
Data in CIF | 2r9x_validation.cif.gz | 53.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/2r9x ftp://data.pdbj.org/pub/pdb/validation_reports/r9/2r9x | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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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: ampC, ampA / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase #2: Chemical | ChemComp-PO4 / #3: Chemical | #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: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.7M KiPO4, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-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 315 / Detector: CCD / Date: Aug 23, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 2.9 % / Av σ(I) over netI: 12.1 / Number: 173290 / Rmerge(I) obs: 0.067 / Χ2: 1.73 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 60696 / % possible obs: 98.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.9→50 Å / Num. obs: 60696 / % possible obs: 98.6 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.067 / Χ2: 1.731 / Net I/σ(I): 12.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.838 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.128 / 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 mean: 20.093 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: 1.903→1.952 Å / Total num. of bins used: 20
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