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Yorodumi- PDB-3c4o: Crystal Structure of the SHV-1 Beta-lactamase/Beta-lactamase inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c4o | ||||||
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Title | Crystal Structure of the SHV-1 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) E73M/S130K/S146M complex | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Beta-lactamase / Beta-lactamase inhibitory protein / protein-protein complex / BLIP / SHV-1 / 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 activity / beta-lactamase / 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: 1.7 Å | ||||||
Authors | Reynolds, K.A. / Hanes, M.S. / Thomson, J.M. / Antczak, A.J. / Berger, J.M. / Bonomo, R.A. / Kirsch, J.F. / Handel, T.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Computational redesign of the SHV-1 beta-lactamase/beta-lactamase inhibitor protein interface. Authors: Reynolds, K.A. / Hanes, M.S. / Thomson, J.M. / Antczak, A.J. / Berger, J.M. / Bonomo, R.A. / Kirsch, J.F. / 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 | 3c4o.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c4o.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 3c4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/3c4o ftp://data.pdbj.org/pub/pdb/validation_reports/c4/3c4o | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28907.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, shv1 / Plasmid: pBCSK(-) / Production host: Escherichia coli (E. coli) / Strain (production host): DH10B / References: UniProt: P0AD64, beta-lactamase | ||
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#2: Protein | Mass: 17644.795 Da / Num. of mol.: 1 / Mutation: E109M,S166K,S182M 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: Chemical | #4: 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: 3.68 Å3/Da / Density % sol: 66.62 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 37.5% Ammonium Sulfate, 100mM Tris HCl, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-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: Mar 7, 2007 |
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: 1.7→50 Å / Num. all: 74627 / Num. obs: 73114 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.098 / Χ2: 1.023 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.442 / Num. unique all: 6300 / Χ2: 1.013 / % possible all: 84.9 |
-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: 1.7→36.224 Å / FOM work R set: 0.892 / Isotropic thermal model: Random / σ(F): 2 / σ(I): 2 / 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: 54.846 Å2 / ksol: 0.373 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 10.55 Å2 / Biso mean: 23.66 Å2 / Biso min: 107.78 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→36.224 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26
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