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Yorodumi- PDB-4rx3: A triple mutant in the omega-loop of TEM-1 beta-lactamase changes... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rx3 | ||||||
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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 catalysis | ||||||
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: 1.39 Å | ||||||
Authors | Stojanoski, V. / Chow, D. / 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 | 4rx3.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rx3.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 4rx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rx3_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
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Full document | 4rx3_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | 4rx3_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 4rx3_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/4rx3 ftp://data.pdbj.org/pub/pdb/validation_reports/rx/4rx3 | HTTPS FTP |
-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: 28882.932 Da / Num. of mol.: 1 / Fragment: TEM-1 beta-lactamase / Mutation: S70G/W165Y/E166Y/P167G 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) / Strain (production host): BL21 (DE3) / References: UniProt: P62593, beta-lactamase |
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#2: Chemical | ChemComp-FLC / |
#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: 2.72 Å3/Da / Density % sol: 54.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.24M citrate, 25% w/v PEG 4,000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: Jun 20, 2014 | ||||||||||||
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Wavelength: 0.997 Å / Relative weight: 1 | ||||||||||||
Reflection | Resolution: 1.39→30.54 Å / Num. all: 64012 / Num. obs: 64012 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 1.9 | ||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→30.54 Å / SU ML: 0.15 / σ(F): 1.92 / Phase error: 18.26 / 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: 1.39→30.54 Å
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Refine LS restraints |
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LS refinement shell |
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