+Open data
-Basic information
Entry | Database: PDB / ID: 4xux | ||||||
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Title | Structure of ampC bound to RPX-7009 at 1.75 A | ||||||
Components | Beta-lactamase | ||||||
Keywords | Hydrolase/antibiotic / Hydrolase-antibiotic 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 | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | ||||||
Authors | Clifton, M.C. / Abendroth, J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Discovery of a Cyclic Boronic Acid beta-Lactamase Inhibitor (RPX7009) with Utility vs Class A Serine Carbapenemases. Authors: Hecker, S.J. / Reddy, K.R. / Totrov, M. / Hirst, G.C. / Lomovskaya, O. / Griffith, D.C. / King, P. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Clifton, M.C. / Atkins, K. / Raymond, ...Authors: Hecker, S.J. / Reddy, K.R. / Totrov, M. / Hirst, G.C. / Lomovskaya, O. / Griffith, D.C. / King, P. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Clifton, M.C. / Atkins, K. / Raymond, A. / Potts, K.T. / Abendroth, J. / Boyer, S.H. / Loutit, J.S. / Morgan, E.E. / Durso, S. / Dudley, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xux.cif.gz | 155.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xux.ent.gz | 118.7 KB | Display | PDB format |
PDBx/mmJSON format | 4xux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xux_validation.pdf.gz | 986.4 KB | Display | wwPDB validaton report |
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Full document | 4xux_full_validation.pdf.gz | 986.6 KB | Display | |
Data in XML | 4xux_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 4xux_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/4xux ftp://data.pdbj.org/pub/pdb/validation_reports/xu/4xux | HTTPS FTP |
-Related structure data
Related structure data | 4xuzC 1xx2S 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 39413.887 Da / Num. of mol.: 1 / Fragment: UNP residues 21-381 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: ampC / Production host: Escherichia coli (E. coli) / References: UniProt: P05364, beta-lactamase | ||||
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#2: Chemical | ChemComp-4D6 / | ||||
#3: Chemical | #4: Chemical | ChemComp-PG0 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.79 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30mg/ml AmpC, 30% PEG3000, 0.1M TRIS, PH 7.0, 0.2M NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 13, 2011 |
Radiation | Monochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 0.9765 |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 34340 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 4.5 / Rejects: 0 / % possible all: 100 |
-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 1XX2 Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.1651 / WRfactor Rwork: 0.1379 / FOM work R set: 0.9055 / SU B: 3.358 / SU ML: 0.059 / SU R Cruickshank DPI: 0.111 / SU Rfree: 0.1039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.104 / 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: 37.64 Å2 / Biso mean: 9.66 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 1.75→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.79 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 10.1439 Å / Origin y: 11.5046 Å / Origin z: 18.3867 Å
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