+Open data
-Basic information
Entry | Database: PDB / ID: 3fkw | ||||||
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Title | AmpC K67R mutant apo structure | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / AmpC / K67R / beta-lactamase / general base / Antibiotic resistance / Periplasm | ||||||
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: 1.498 Å | ||||||
Authors | Chen, Y. / McReynolds, A. / Shoichet, B.K. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Re-examining the role of Lys67 in class C beta-lactamase catalysis. Authors: Chen, Y. / McReynolds, A. / 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 | 3fkw.cif.gz | 327.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fkw.ent.gz | 266.8 KB | Display | PDB format |
PDBx/mmJSON format | 3fkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/3fkw ftp://data.pdbj.org/pub/pdb/validation_reports/fk/3fkw | HTTPS FTP |
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-Related structure data
Related structure data | 3fkvC 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 39615.938 Da / Num. of mol.: 2 / Fragment: residues 20-377 / Mutation: K67R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ampA, ampC, b4150, JW4111 / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase #2: Chemical | #3: Chemical | ChemComp-K / | #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: 2.51 Å3/Da / Density % sol: 51.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: Potassium Phosphate, pH 8.7, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 25, 2006 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.498→88.05 Å / Num. obs: 120185 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.051 / Χ2: 1.048 / Net I/σ(I): 16.662 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1KE4 Resolution: 1.498→88.05 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.178 / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.88 / SU B: 2.665 / SU ML: 0.046 / SU R Cruickshank DPI: 0.093 / SU Rfree: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 56.55 Å2 / Biso mean: 18.082 Å2 / Biso min: 7.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.498→88.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.498→1.537 Å / Total num. of bins used: 20
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