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Yorodumi- PDB-261l: STRUCTURAL CHARACTERISATION OF AN ENGINEERED TANDEM REPEAT CONTRA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 261l | ||||||
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Title | STRUCTURAL CHARACTERISATION OF AN ENGINEERED TANDEM REPEAT CONTRASTS THE IMPORTANCE OF CONTEXT AND SEQUENCE IN PROTEIN FOLDING | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / HYDROLASE (O-GLYCOSYL) / T4 LYSOZYME / ENGINEERED TANDEM REPEAT / PROTEIN ENGINEERING / PROTEIN DESIGN | ||||||
Function / homology | Function and homology information viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sagermann, M. / Baase, W.A. / Matthews, B.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Structural characterization of an engineered tandem repeat contrasts the importance of context and sequence in protein folding. Authors: Sagermann, M. / Baase, W.A. / Matthews, B.W. #1: Journal: Protein Sci. / Year: 1998 Title: Protein Structural Plasticity Examplified by Insertion and Deletion Authors: Vetter, I.R. / Baase, W.A. / Heinz, D. / Xiong, J.P. / Snow, S. / Matthews, B.W. #2: Journal: Nature / Year: 1993 Title: Folding and Function of a T4 Lysosyme Containing 10 Consecutive Alanines Illustrate the Redundancy of Information in an Amino Acid Sequence Authors: Heinz, D. / Baase, W.A. / Dahlquist, F.W. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 261l.cif.gz | 47 KB | Display | PDBx/mmCIF format |
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PDB format | pdb261l.ent.gz | 33.3 KB | Display | PDB format |
PDBx/mmJSON format | 261l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/61/261l ftp://data.pdbj.org/pub/pdb/validation_reports/61/261l | HTTPS FTP |
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-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: 19544.395 Da / Num. of mol.: 1 / Mutation: L39I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato Description: BACTERIOPHAGE T4 (MUTANT GENE DERIVED FROM THE M13 PLASMID BY CLONING THE T4 LY SOZYME GENE) Cellular location: CYTOPLASM / Gene: GENE E FROM BACTERIOPHAGE T4 / Plasmid: PHS1403 / Gene (production host): T4 LYSOZYME / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme |
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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: 2.98 Å3/Da / Density % sol: 58 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: CRYSTALS WERE GROWN FROM 20% POLYETHYLENE GLYCOL 6000, 20% ISOPROPANOL, 50MM TRIS-HCL PH 7.5 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient pressure: 101 kPa / Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 0.908 Å |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 28161 / % possible obs: 86.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.084 |
Reflection shell | Highest resolution: 2.5 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CYS-FREE VERSION OF T4-LYSOZYME Resolution: 2.5→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: GROUPED OCCUPANCY REFINEMENT ONLY FOR RESIDUES 36-40
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Solvent computation | Solvent model: BABENET SCALING / Bsol: 150 Å2 / ksol: 0.7 e/Å3 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5F / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.17 / Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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