[English] 日本語
Yorodumi- PDB-4bjs: Crystal structure of the Rif1 C-terminal domain (Rif1-CTD) from S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bjs | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Rif1 C-terminal domain (Rif1-CTD) from Saccharomyces cerevisiae | ||||||
Components | (TELOMERE LENGTH REGULATOR PROTEIN RIF1) x 2 | ||||||
Keywords | CELL CYCLE / TELOMERE ASSOCIATED PROTEINS | ||||||
Function / homology | Function and homology information negative regulation of mitotic DNA replication initiation from late origin / regulation of DNA stability / shelterin complex / centromeric DNA binding / DNA double-strand break processing / telomere capping / silent mating-type cassette heterochromatin formation / protein localization to chromosome, telomeric region / telomeric DNA binding / DNA replication origin binding ...negative regulation of mitotic DNA replication initiation from late origin / regulation of DNA stability / shelterin complex / centromeric DNA binding / DNA double-strand break processing / telomere capping / silent mating-type cassette heterochromatin formation / protein localization to chromosome, telomeric region / telomeric DNA binding / DNA replication origin binding / DNA replication initiation / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of DNA-templated DNA replication initiation / telomere maintenance / chromosome, telomeric region / nucleus Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.94 Å | ||||||
Authors | Bunker, R.D. / Shi, T. / Gut, H. / Scrima, A. / Thoma, N.H. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2013 Title: Rif1 and Rif2 Shape Telomere Funcation and Architecture Through Multivalent RAP1 Interactions Authors: Shi, T. / Bunker, R.D. / Mattarocci, S. / Ribeyre, C. / Faty, M. / Gut, H. / Scrima, A. / Rass, U. / Rubin, S.M. / Shore, D. / Thoma, N.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4bjs.cif.gz | 182.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4bjs.ent.gz | 149.9 KB | Display | PDB format |
PDBx/mmJSON format | 4bjs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bjs_validation.pdf.gz | 436.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4bjs_full_validation.pdf.gz | 436.6 KB | Display | |
Data in XML | 4bjs_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 4bjs_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/4bjs ftp://data.pdbj.org/pub/pdb/validation_reports/bj/4bjs | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 7216.321 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN (RIF1-CTD, RESIDUES 1857-1916) Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29539 #2: Protein | | Mass: 7230.347 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (RIF1-CTD, RESIDUES 1857-1916) Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29539 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40 % / Description: NONE |
---|---|
Crystal grow | Details: 20% (W/V) PEG 3000, 200 MM NACL, 100 HEPES/NAOH PH 7.5. PROTEIN WAS TREATED WITH 0.003% TRYPSIN IMMEDIATELY PRIOR TO CRYSTALLIZATION. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→45.5 Å / Num. obs: 15001 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 17.66 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.94→1.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 73.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: DIRECT METHODS Starting model: 14-MER POLY-ALA IDEALIZED ALPHA-HELIX Resolution: 1.94→17.26 Å / Cor.coef. Fo:Fc: 0.9368 / Cor.coef. Fo:Fc free: 0.9174 / SU R Cruickshank DPI: 0.897 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.168 / SU Rfree Blow DPI: 0.135 / SU Rfree Cruickshank DPI: 0.138
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.39 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.192 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→17.26 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.94→2.07 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 10.8206 Å / Origin y: 41.6249 Å / Origin z: 33.4246 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: ALL |