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- PDB-4bjt: Crystal structure of the Rap1 C-terminal domain (Rap1-RCT) in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bjt | ||||||
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Title | Crystal structure of the Rap1 C-terminal domain (Rap1-RCT) in complex with the Rap1 binding module of Rif1 (Rif1-RBM) | ||||||
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Function / homology | ![]() negative regulation of mitotic DNA replication initiation from late origin / positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / regulation of DNA stability / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shi, T. / Bunker, R.D. / Gut, H. / Scrima, A. / Thoma, N.H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 390 KB | Display | ![]() |
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PDB format | ![]() | 323.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4bj1C ![]() 4bj5C ![]() 4bj6C ![]() 4bjsC ![]() 3owtS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 23248.975 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN RAP1-RCT, RESIDUES 672-827 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 2286.732 Da / Num. of mol.: 3 / Fragment: RAP1 BINDING MODULE, RESIDUES 1752-1771 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67 % / Description: NONE |
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Crystal grow![]() | Details: 2.4-2.5 M AMMONIUM SULFATE, 100 MM NA CITRATE PH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2011 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE-CRYSTAL SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.61→47 Å / Num. obs: 103829 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 23.98 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.61→1.62 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.3 / % possible all: 88.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3OWT Resolution: 1.61→47.16 Å / Cor.coef. Fo:Fc: 0.9515 / Cor.coef. Fo:Fc free: 0.9378 / SU R Cruickshank DPI: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.064 / SU Rfree Blow DPI: 0.064 / SU Rfree Cruickshank DPI: 0.064 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 31.03 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→47.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.65 Å / Total num. of bins used: 20
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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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