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Yorodumi- PDB-1oyu: Long-Distance conformational changes in a protein engineered by m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oyu | ||||||
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Title | Long-Distance conformational changes in a protein engineered by modulated sequence duplication | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / sequence duplication / design of structural switches / tandem repeat / 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. / Gay, L. / Matthews, B.W. | ||||||
Citation | 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. #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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oyu.cif.gz | 81.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oyu.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 1oyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oyu_validation.pdf.gz | 437.8 KB | Display | wwPDB validaton report |
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Full document | 1oyu_full_validation.pdf.gz | 461.6 KB | Display | |
Data in XML | 1oyu_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 1oyu_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/1oyu ftp://data.pdbj.org/pub/pdb/validation_reports/oy/1oyu | HTTPS FTP |
-Related structure data
Related structure data | 3lzmS 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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2 |
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Unit cell |
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Details | Two molecules in the asymmetric unit, A and B, refinement was carried out in the absence of NCS relationship |
-Components
#1: Protein | Mass: 19513.361 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 / Plasmid: phs1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / 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: 2.49 Å3/Da / Density % sol: 50.7 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% poly-ethylene glycol 4000, 50mM phosphate buffer, 0.2mM ammonium acetate, 20% isopropanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 170 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.99 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 2001 / Details: mirrors |
Radiation | Monochromator: Flat mirror, single SI crystal bend / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→36.62 Å / Num. obs: 13538 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 43.7 Å2 / Rsym value: 0.072 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5.21 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2047 / Rsym value: 0.22 / % possible all: 96.6 |
Reflection | *PLUS Num. obs: 12441 / Rmerge(I) obs: 0.072 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3lzm Resolution: 2.5→37 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: In molecule A, the density between residues 53-64 is very poor. The occupancy of these atoms has been set to zero. In Molecule B, the density for the main chain was clearly visible in OMIT ...Details: In molecule A, the density between residues 53-64 is very poor. The occupancy of these atoms has been set to zero. In Molecule B, the density for the main chain was clearly visible in OMIT maps, however, the density is weak and no side chain density could be identified. After several trials of refinement, the occupancy has been set to 0.6 for atoms of residues 53-64. Also, the final amino acids Asn174 and Leu175 could not be localized in the structure.
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→37 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1.1 / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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