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Yorodumi- PDB-3e2k: Crystal Structure of the KPC-2 Beta-lactamase/Beta-lactamase inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e2k | ||||||
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Title | Crystal Structure of the KPC-2 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Beta-lactamase / Beta-lactamase inhibitor protein / protein-protein complex / BLIP / KPC-2 / Antibiotic resistance / Hydrolase / Plasmid / Secreted / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information regulation of beta-lactamase activity / beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic / extracellular region Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) Streptomyces clavuligerus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Hanes, M.S. / Jude, K.M. / Berger, J.M. / Bonomo, R.A. / Handel, T.M. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural and biochemical characterization of the interaction between KPC-2 beta-lactamase and beta-lactamase inhibitor protein Authors: Hanes, M.S. / Jude, K.M. / Berger, J.M. / Bonomo, R.A. / Handel, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e2k.cif.gz | 166 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e2k.ent.gz | 136.5 KB | Display | PDB format |
PDBx/mmJSON format | 3e2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/3e2k ftp://data.pdbj.org/pub/pdb/validation_reports/e2/3e2k | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27993.451 Da / Num. of mol.: 2 / Fragment: UNP residues 30-293 / Mutation: G175S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: KPC-2, blaKPC-2 / Plasmid: pET24a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q93LQ9, UniProt: Q9F663*PLUS, beta-lactamase #2: Protein | Mass: 17556.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35804 #3: 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: 2.08 Å3/Da / Density % sol: 40.9 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20% PEG 8000, 4% ethylene glycol, 100mM citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 6, 2008 |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 46315 / Num. obs: 46291 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.127 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.689 / % 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 / Resolution: 2.1→40.777 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.5 / σ(F): 1.33 / Phase error: 23.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.318 Å2 / ksol: 0.376 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.913 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→40.777 Å
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Refine LS restraints |
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LS refinement shell |
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