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Yorodumi- PDB-4op5: Crystal structure of stabilized TEM-1 beta-lactamase variant v.13... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4op5 | ||||||
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Title | Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying R164S mutation | ||||||
Components | Extended spectrum beta-lactamase TEM-63 | ||||||
Keywords | HYDROLASE / Beta-lactamase | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | ||||||
Authors | Dellus-Gur, E. / Elias, M. / Fraser, J.S. / Tawfik, D.S. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2015 Title: Negative Epistasis and Evolvability in TEM-1 beta-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder. Authors: Dellus-Gur, E. / Elias, M. / Caselli, E. / Prati, F. / Salverda, M.L. / de Visser, J.A. / Fraser, J.S. / Tawfik, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4op5.cif.gz | 135.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4op5.ent.gz | 104 KB | Display | PDB format |
PDBx/mmJSON format | 4op5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/4op5 ftp://data.pdbj.org/pub/pdb/validation_reports/op/4op5 | HTTPS FTP |
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-Related structure data
Related structure data | 4op8C 4opqC 4oprC 4opyC 4opzC 4oq0C 4oqgC 4oqhC 4oqiC 1zg4S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28700.662 Da / Num. of mol.: 1 / Fragment: TEM-1 Mutation: R164S, A42G, N52A, I84V, R120G, M182T, L201A, T265M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaTEM-63 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AGJ5 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-PG4 / |
#4: Chemical | ChemComp-MES / |
#5: 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: 2.12 Å3/Da / Density % sol: 42.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 9% (wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES pH 6.2, and 200mM Ca(OAc)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.7999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7999 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→44.15 Å / Num. all: 360642 / Num. obs: 109005 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 3.31 % / Rsym value: 0.036 / Net I/σ(I): 16.45 |
Reflection shell | Redundancy: 3.21 % / Rsym value: 0.397 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZG4 Resolution: 1.05→44.15 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.714 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 13.864 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→44.15 Å
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Refine LS restraints |
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