+Open data
-Basic information
Entry | Database: PDB / ID: 4bj1 | ||||||
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Title | Crystal structure of Saccharomyces cerevisiae RIF2 | ||||||
Components | PROTEIN RIF2 | ||||||
Keywords | DNA BINDING PROTEIN / GENOME STABILITY / TELOMERE ASSOCIATED PROTEINS / AAA+ FOLD | ||||||
Function / homology | Function and homology information shelterin complex / telomere capping / telomeric DNA binding / telomere maintenance via telomerase / telomere maintenance / chromosome, telomeric region Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.94 Å | ||||||
Authors | Shi, T. / Bunker, R.D. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bj1.cif.gz | 115.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bj1.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 4bj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/4bj1 ftp://data.pdbj.org/pub/pdb/validation_reports/bj/4bj1 | HTTPS FTP |
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-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: 36800.336 Da / Num. of mol.: 1 / Fragment: RESIDUES 65-380 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Plasmid: PGEX BASED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06208 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 0.64 % / Description: NONE |
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Crystal grow | Details: 14-20% 1,4-BUTANEDIOL, 100 MM NA ACETATE PH 5.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 17, 2009 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE-CRYSTAL SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→44.5 Å / Num. obs: 9796 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 105.55 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.94→2.95 Å / Redundancy: 8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.4 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.94→38.65 Å / Cor.coef. Fo:Fc: 0.9396 / Cor.coef. Fo:Fc free: 0.9311 / SU R Cruickshank DPI: 0.696 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.881 / SU Rfree Blow DPI: 0.314 / SU Rfree Cruickshank DPI: 0.31 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 95.39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.497 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.94→38.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.94→3.29 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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