[English] 日本語
Yorodumi- PDB-2f32: Xray crystal structure of lysozyme mutant L20/R63A liganded to et... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f32 | ||||||
---|---|---|---|---|---|---|---|
Title | Xray crystal structure of lysozyme mutant L20/R63A liganded to ethylguanidinium | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Yousef, M.S. / Bischoff, N. / Dyer, C.M. / Baase, W.A. / Matthews, B.W. | ||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: Guanidinium derivatives bind preferentially and trigger long-distance conformational changes in an engineered T4 lysozyme. Authors: Yousef, M.S. / Bischoff, N. / Dyer, C.M. / Baase, W.A. / Matthews, B.W. #1: 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. #2: 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. #3: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2f32.cif.gz | 53.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2f32.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 2f32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f32_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2f32_full_validation.pdf.gz | 453.5 KB | Display | |
Data in XML | 2f32_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 2f32_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/2f32 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/2f32 | HTTPS FTP |
-Related structure data
Related structure data | 2f2qC 2f47C 1t8aS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19685.541 Da / Num. of mol.: 1 / Mutation: L39I, INS (NAAKSELDKAI -N62), R63A, C65T, C108A 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 / Plasmid: pHS 1405 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme |
---|---|
#2: Chemical | ChemComp-BME / |
#3: Chemical | ChemComp-EGD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53 % |
---|---|
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 ETHYL GUANIDINIUM CHLORIDE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 19758 / % possible obs: 99 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 0.07 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.36 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T8A Resolution: 1.8→27.38 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 569234.74 / Data cutoff high rms absF: 569234.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.4182 Å2 / ksol: 0.348392 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→27.38 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|