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Yorodumi- PDB-1t8a: USE OF SEQUENCE DUPLICATION TO ENGINEER A LIGAND-TRIGGERED LONG-D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t8a | ||||||
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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-BITECHNOLOGY / 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 / MOLECULAR REPLACEMENT / Resolution: 2 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: Proc.Natl.Acad.Sci.USA / 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 | 1t8a.cif.gz | 51.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t8a.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 1t8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t8a_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
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Full document | 1t8a_full_validation.pdf.gz | 452.5 KB | Display | |
Data in XML | 1t8a_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 1t8a_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/1t8a ftp://data.pdbj.org/pub/pdb/validation_reports/t8/1t8a | HTTPS FTP |
-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: 19685.541 Da / Num. of mol.: 1 / Mutation: L39I, R63A, C54T,C97A 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 |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-GAI / |
#4: Chemical | ChemComp-HED / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8 M MIXED POTASSIUM AND SODIUM PHOSPHATE. 0.2 M GUANIDINIUM CHLORIDE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: KOHZU: DOUBLE CRYSTAL SI(111) |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 13956 / % possible obs: 99 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.046 / Net I/σ(I): 33 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 5 / Rsym value: 0.214 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 596848.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.8516 Å2 / ksol: 0.376985 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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