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Yorodumi- PDB-5nvr: Crystal structure of the Rif1 N-terminal domain (RIF1-NTD) from S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nvr | ||||||
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Title | Crystal structure of the Rif1 N-terminal domain (RIF1-NTD) from Saccharomyces cerevisiae | ||||||
Components | Telomere length regulator protein RIF1 | ||||||
Keywords | STRUCTURAL PROTEIN / telomere maintenance / DNA double-strand break repair / irregular helical repeat / all-alpha fold | ||||||
Function / homology | Function and homology information negative regulation of mitotic DNA replication initiation from late origin / regulation of DNA stability / DNA double-strand break processing / shelterin complex / telomere capping / silent mating-type cassette heterochromatin formation / protein localization to chromosome, telomeric region / telomeric DNA binding / DNA replication initiation / negative regulation of DNA-templated DNA replication initiation ...negative regulation of mitotic DNA replication initiation from late origin / regulation of DNA stability / DNA double-strand break processing / shelterin complex / telomere capping / silent mating-type cassette heterochromatin formation / protein localization to chromosome, telomeric region / telomeric DNA binding / DNA replication initiation / negative regulation of DNA-templated DNA replication initiation / telomere maintenance / chromosome, telomeric region / cell cycle / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.95 Å | ||||||
Authors | Bunker, R.D. / Shi, T. / Thoma, N.H. | ||||||
Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2017 Title: Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends. Authors: Mattarocci, S. / Reinert, J.K. / Bunker, R.D. / Fontana, G.A. / Shi, T. / Klein, D. / Cavadini, S. / Faty, M. / Shyian, M. / Hafner, L. / Shore, D. / Thoma, N.H. / Rass, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nvr.cif.gz | 653.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nvr.ent.gz | 574.2 KB | Display | PDB format |
PDBx/mmJSON format | 5nvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/5nvr ftp://data.pdbj.org/pub/pdb/validation_reports/nv/5nvr | HTTPS FTP |
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-Related 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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-Components
#1: Protein | Mass: 129054.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RIF1, YBR275C, YBR1743 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29539 |
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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: 4.62 Å3/Da / Density % sol: 73.39 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3.8 mg/ml protein solution in 50 mM HEPES pH 7.4, 310 mM NaCl, 1 mM TCEP mixed equally (1 uL + 1 uL) with 100 mM Tris-HCl, pH 7.5, 320 mM lithium sulfate, 850 mM potassium sodium tartrate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97902 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 22, 2012 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97902 Å / Relative weight: 1 |
Reflection | Resolution: 3.94→49.43 Å / Num. obs: 21894 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 50.6 % / Biso Wilson estimate: 183 Å2 / Rmerge(I) obs: 0.234 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 3.94→4.16 Å / Redundancy: 42.7 % / Rmerge(I) obs: 4.131 / Mean I/σ(I) obs: 1.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.95→49.3 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 28.57 Details: ANOMALOUS PAIRS SEPARATED FOR REFINEMENT AND MLHL REFINEMENT TARGET USED WITH SE-SAD PHASE RESTRAINTS CALCULATED BY MR-SAD WITH PHASER. TLS ONLY ATOMIC DISPLACEMENT MODEL APPLIED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 221 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.95→49.3 Å
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Refine LS restraints |
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LS refinement shell |
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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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