[English] 日本語
Yorodumi- PDB-1uw3: The crystal structure of the globular domain of sheep prion protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uw3 | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of the globular domain of sheep prion protein | ||||||
Components | PRION PROTEINPRNP | ||||||
Keywords | MEMBRANE PROTEIN / TRANSMISSIBLE SPONGIFORM ENCEPHALOPATHY / CREUTZFELD JACOB DISEASE | ||||||
Function / homology | Function and homology information side of membrane / tubulin binding / protein homooligomerization / microtubule binding / copper ion binding / Golgi apparatus / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | OVIS ARIES (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Haire, L.F. / Whyte, S.M. / Vasisht, N. / Gill, A.C. / Verma, C. / Dodson, E.J. / Dodson, G.G. / Bayley, P.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: The Crystal Structure of the Globular Domain of Sheep Prion Protein Authors: Haire, L.F. / Whyte, S.M. / Vasisht, N. / Gill, A.C. / Verma, C. / Dodson, E.J. / Dodson, G.G. / Bayley, P.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1uw3.cif.gz | 37.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1uw3.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 1uw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/1uw3 ftp://data.pdbj.org/pub/pdb/validation_reports/uw/1uw3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1i4mS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 12609.001 Da / Num. of mol.: 1 / Fragment: RESIDUES 128-233 / Source method: isolated from a natural source / Source: (natural) OVIS ARIES (sheep) / References: UniProt: P23907 |
---|---|
#2: Chemical | ChemComp-GSH / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.6 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8.6 / Details: pH 8.60 | ||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 8.6 / PH range high: 7.4 | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 165 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.414 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.414 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→19.3 Å / Num. obs: 7095 / % possible obs: 93.2 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.05→2.13 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 78 |
Reflection | *PLUS Highest resolution: 2.05 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS % possible obs: 83.7 % / Rmerge(I) obs: 0.465 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I4M Resolution: 2.05→84.51 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.829 / SU B: 5.928 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: RESIDUES 125 - 137 ARE POORLY ORDERED, AND PROBABLY TAKE UP MORE THAN ONE CONFORMATION.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.69 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→84.51 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|