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Yorodumi- PDB-3dtm: Increased folding stability of TEM-1 beta-lactamase by in-vitro s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dtm | ||||||
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Title | Increased folding stability of TEM-1 beta-lactamase by in-vitro selection | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / TEM-1 Beta-Lactamase / Antibiotic resistance / Plasmid | ||||||
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 Å | ||||||
Authors | Kather, I. / Jakob, R.P. / Dobbek, H. / Schmid, F.X. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dtm.cif.gz | 64.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dtm.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 3dtm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/3dtm ftp://data.pdbj.org/pub/pdb/validation_reports/dt/3dtm | HTTPS FTP |
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-Related structure data
Related structure data | 1btlS S: Starting model for refinement |
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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: 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.) Escherichia coli (E. coli) / Strain: BL21 DE3 / Plasmid: pTAC11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 References: UniProt: Q79DR3, UniProt: P62593*PLUS, beta-lactamase |
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#2: 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: 2.39 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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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