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Yorodumi- PDB-4ibr: Crystal structure of stabilized TEM-1 beta-lactamase variant v.13... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ibr | ||||||
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Title | Crystal structure of stabilized TEM-1 beta-lactamase variant v.13 carrying G238S/E104K mutations | ||||||
Components | TEM-94 ES-beta-lactamase | ||||||
Keywords | HYDROLASE / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dellus-Gur, E. / Toth-Petroczy, A. / Elias, M. / Tawfik, D.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: What Makes a Protein Fold Amenable to Functional Innovation? Fold Polarity and Stability Trade-offs. Authors: Dellus-Gur, E. / Toth-Petroczy, A. / Elias, M. / 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 | 4ibr.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ibr.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ibr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ibr_validation.pdf.gz | 442.4 KB | Display | wwPDB validaton report |
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Full document | 4ibr_full_validation.pdf.gz | 446.6 KB | Display | |
Data in XML | 4ibr_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4ibr_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/4ibr ftp://data.pdbj.org/pub/pdb/validation_reports/ib/4ibr | HTTPS FTP |
-Related structure data
Related structure data | 4ibxC 1zg4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: 28800.873 Da / Num. of mol.: 1 Mutation: A41G, N51A, R119G, M181T, L200A, T262M, G237S, E103K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla-TEM-94 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-MES / |
#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: 2.14 Å3/Da / Density % sol: 42.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 11% (wt/vol) polyethylene glycol (PEG) 8000, 100 mM MES buffer pH 6.7, 200mM Ca(OAc)2 and 10 M ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 13, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→80 Å / Num. all: 12590 / Num. obs: 12175 / % possible obs: 96.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rsym value: 0.113 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZG4 Resolution: 2.2→67.96 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.55 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.164 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→67.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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