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- PDB-3dtm: Increased folding stability of TEM-1 beta-lactamase by in-vitro s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dtm | ||||||
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Title | Increased folding stability of TEM-1 beta-lactamase by in-vitro selection | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / TEM-1 Beta-Lactamase / Antibiotic resistance / Plasmid | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kather, I. / Jakob, R.P. / Dobbek, H. / Schmid, F.X. | ||||||
![]() | ![]() Title: Increased folding stability of TEM-1 beta-lactamase by in vitro selection Authors: Kather, I. / Jakob, R.P. / Dobbek, H. / Schmid, F.X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.2 KB | Display | ![]() |
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PDB format | ![]() | 46.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.4 KB | Display | ![]() |
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Full document | ![]() | 423.5 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1btlS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28857.896 Da / Num. of mol.: 1 / Fragment: UNP residues 24-286 Mutation: P62S, V80I, E147G, M182T, L201P, I208M, A224V, I246V, L273R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q79DR3, UniProt: P62593*PLUS, beta-lactamase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.61 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6-1.8 M Ammonium citrate, 5% PEG 400, 0.1M Tris buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 8, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→19.59 Å / Num. all: 23406 / Num. obs: 23406 / % possible obs: 99.75 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 8.3 |
Reflection shell | Resolution: 1.86→1.9 Å / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1056 / Rsym value: 0.348 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BTL Resolution: 2→19.41 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.83 / SU B: 5.063 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.189 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 6.495 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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