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Yorodumi- PDB-4kg5: Crystal Structure of AmpC beta-lactamase N152G Mutant in Complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kg5 | |||||||||
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Title | Crystal Structure of AmpC beta-lactamase N152G Mutant in Complex with Cefotaxime | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | Hydrolase/antibiotic / Cephalosporinase / beta-lactamase / serine hydrolase / acyl-enzyme complex / 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 | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | |||||||||
Authors | Docter, B.E. / Baggett, V.L. / Powers, R.A. / Wallar, B.J. | |||||||||
Citation | Journal: To be Published Title: Complexed structures of AmpC beta-lactamase Authors: Docter, B.E. / Baggett, V.L. / Powers, R.A. / Wallar, B.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kg5.cif.gz | 288.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kg5.ent.gz | 243.6 KB | Display | PDB format |
PDBx/mmJSON format | 4kg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kg5_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4kg5_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4kg5_validation.xml.gz | 56.1 KB | Display | |
Data in CIF | 4kg5_validation.cif.gz | 79.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/4kg5 ftp://data.pdbj.org/pub/pdb/validation_reports/kg/4kg5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 39530.871 Da / Num. of mol.: 4 / Mutation: N152G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ampC, ampA, b4150, JW4111 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / References: UniProt: P00811, beta-lactamase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-CEF / #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: 2.61 Å3/Da / Density % sol: 52.94 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.7M potassium phosphate, 3.5mg/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: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→50 Å / Num. obs: 91517 |
Reflection shell | Resolution: 2.11→2.18 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→28.23 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.155 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.185 / 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: 36.593 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→28.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.162 Å / Total num. of bins used: 20
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