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Yorodumi- PDB-4jxs: X-ray crystal structure of AmpC beta-lactamase from E. coli in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jxs | ||||||
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Title | X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with a non-covalent inhibitor 3-[(4-CARBOXYBENZYL)SULFAMOYL]THIOPHENE-2-CARBOXYLIC ACID (compound 4) | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / cephalosporinase / beta-lactamase / serine hydrolase / beta-lactamase inhibitor complex / 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: 1.9 Å | ||||||
Authors | Powers, R.A. / Hendershot, J.M. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2014 Title: Structure-based efforts to optimize a non-beta-lactam inhibitor of AmpC beta-lactamase. Authors: Hendershot, J.M. / Mishra, U.J. / Smart, R.P. / Schroeder, W. / Powers, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jxs.cif.gz | 156.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jxs.ent.gz | 122.6 KB | Display | PDB format |
PDBx/mmJSON format | 4jxs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jxs_validation.pdf.gz | 754.9 KB | Display | wwPDB validaton report |
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Full document | 4jxs_full_validation.pdf.gz | 760.1 KB | Display | |
Data in XML | 4jxs_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 4jxs_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/4jxs ftp://data.pdbj.org/pub/pdb/validation_reports/jx/4jxs | HTTPS FTP |
-Related structure data
Related structure data | 4jxvC 4jxwC 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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1 |
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2 |
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3 |
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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: ampC, ampA, b4150, JW4111 / Plasmid: pOGO95 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase #2: Chemical | #3: Chemical | ChemComp-18U / | #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: 2.52 Å3/Da / Density % sol: 51.26 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.7 M potassium phosphate; 3.5 mg/mL AmpC , pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 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: 1.9→50 Å / Num. obs: 62237 / % possible obs: 99.9 % |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KE4 Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.751 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.13 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.794 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.895→1.944 Å / Total num. of bins used: 20
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