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Yorodumi- PDB-4rva: A triple mutant in the omega-loop of TEM-1 beta-lactamase changes... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rva | ||||||
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Title | A triple mutant in the omega-loop of TEM-1 beta-lactamase changes the substrate profile via a large conformational change and an altered general base for deacylation | ||||||
Components | Beta-lactamase TEM | ||||||
Keywords | HYDROLASE / globular / beta-lactamase | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4397 Å | ||||||
Authors | Stojanoski, V. / Chow, D.-C. / Hu, L. / Sankaran, B. / Gilbert, H. / Prasad, B.V.V. / Palzkill, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: A Triple Mutant in the Omega-loop of TEM-1 beta-Lactamase Changes the Substrate Profile via a Large Conformational Change and an Altered General Base for Catalysis. Authors: Stojanoski, V. / Chow, D.C. / Hu, L. / Sankaran, B. / Gilbert, H.F. / Prasad, B.V. / Palzkill, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rva.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rva.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 4rva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/4rva ftp://data.pdbj.org/pub/pdb/validation_reports/rv/4rva | HTTPS FTP |
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-Related structure data
Related structure data | 4rx2C 4rx3C 1btlS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 28896.912 Da / Num. of mol.: 1 / Fragment: TEM-1 / Mutation: W165Y/E166Y/P167G/L201P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase |
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#2: Chemical | ChemComp-BCT / |
#3: 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: 2.62 Å3/Da / Density % sol: 53.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG 3350, 0.2M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 200 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.997 Å | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2014 | ||||||||||||||||||
Radiation | Monochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.997 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.4397→59.51 Å / Num. obs: 55742 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BTL Resolution: 1.4397→48.981 Å / SU ML: 0.14 / σ(F): 1.91 / Phase error: 18.38 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4397→48.981 Å
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Refine LS restraints |
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LS refinement shell |
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