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Yorodumi- PDB-1t97: Use of sequence duplication to engineer a ligand-triggered long-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t97 | ||||||
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Title | Use of sequence duplication to engineer a ligand-triggered long-distance molecular switch in T4 Lysozyme | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / MOLECULAR SWITCH / T4 LYSOZYME / NANO-BIOTECHNOLOGY / PROTEIN ENGINEERING / PROTEIN DESIGN / SEQUENCE DUPLICATION | ||||||
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: 2.7 Å | ||||||
Authors | Yousef, M.S. / Baase, W.A. / Matthews, B.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Use of sequence duplication to engineer a ligand-triggered, long-distance molecular switch in T4 lysozyme. Authors: Yousef, M.S. / Baase, W.A. / Matthews, B.W. #1: 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. #2: Journal: Plant Mol.Biol. / Year: 2003 Title: Long-distance conformational changes in a protein engineered by modulated sequence duplication. Authors: Sagermann, M. / Gay, L. / 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 | 1t97.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t97.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 1t97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t97_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 1t97_full_validation.pdf.gz | 457.6 KB | Display | |
Data in XML | 1t97_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 1t97_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/1t97 ftp://data.pdbj.org/pub/pdb/validation_reports/t9/1t97 | HTTPS FTP |
-Related 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
#1: Protein | Mass: 19685.541 Da / Num. of mol.: 2 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 / Gene: E / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.7 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% POLY-ETHYLENE GLYCOL 3400, 100MM HEPES BUFFER, 200MM AMMONIUM ACETATE, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 11359 / % possible obs: 99 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 36.7 Å2 / Rsym value: 0.067 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.7→2.8 Å / Mean I/σ(I) obs: 7 / Rsym value: 0.15 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 420103.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: FOR MONOMER "A", THERE WAS NO VISIBLE DENSITY FOR RESIDUES 54-61 THERFORE THEY WERE NOT MODELED.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.6322 Å2 / ksol: 0.331785 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.9 Å / Total num. of bins used: 6 /
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Xplor file |
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