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Yorodumi- PDB-6t9q: Crystal structure of the second, C-terminal repeat of the DNA-bin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t9q | ||||||
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Title | Crystal structure of the second, C-terminal repeat of the DNA-binding domain of human TImeless | ||||||
Components | Protein timeless homolog | ||||||
Keywords | REPLICATION / DNA-binding / 3-helix bundle / tandem repeat | ||||||
Function / homology | Function and homology information cellular response to bleomycin / detection of abiotic stimulus / replication fork arrest / cell cycle phase transition / cellular response to cisplatin / cellular response to hydroxyurea / DNA replication checkpoint signaling / replication fork protection complex / positive regulation of double-strand break repair / branching morphogenesis of an epithelial tube ...cellular response to bleomycin / detection of abiotic stimulus / replication fork arrest / cell cycle phase transition / cellular response to cisplatin / cellular response to hydroxyurea / DNA replication checkpoint signaling / replication fork protection complex / positive regulation of double-strand break repair / branching morphogenesis of an epithelial tube / positive regulation of double-strand break repair via homologous recombination / morphogenesis of an epithelium / lung development / regulation of circadian rhythm / circadian rhythm / site of double-strand break / Processing of DNA double-strand break ends / cell division / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / chromatin / DNA binding / nucleoplasm / nucleus / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å | ||||||
Authors | Pellegrini, L. / Holzer, S. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Embo J. / Year: 2020 Title: Timeless couples G-quadruplex detection with processing by DDX11 helicase during DNA replication. Authors: Lerner, L.K. / Holzer, S. / Kilkenny, M.L. / Svikovic, S. / Murat, P. / Schiavone, D. / Eldridge, C.B. / Bittleston, A. / Maman, J.D. / Branzei, D. / Stott, K. / Pellegrini, L. / Sale, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t9q.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t9q.ent.gz | 42.7 KB | Display | PDB format |
PDBx/mmJSON format | 6t9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/6t9q ftp://data.pdbj.org/pub/pdb/validation_reports/t9/6t9q | 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: 7876.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The DP dipeptide at the start of the sequence is part of the leftover of the expression tag after protease cleavage Source: (gene. exp.) Homo sapiens (human) / Gene: TIMELESS, TIM, TIM1, TIMELESS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNS1 |
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#2: 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: 2.34 Å3/Da / Density % sol: 47.52 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / Details: 200mM Sodium formate 18% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→31.46 Å / Num. obs: 25072 / % possible obs: 96.33 % / Redundancy: 4.2 % / Biso Wilson estimate: 11.3 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.1377 / Rpim(I) all: 0.06851 / Rrim(I) all: 0.1543 / Net I/σ(I): 6.82 |
Reflection shell | Resolution: 1.15→1.191 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.4873 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 1920 / CC1/2: 0.464 / Rpim(I) all: 0.4274 / Rrim(I) all: 0.6505 / % possible all: 74.84 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.15→31.46 Å / SU ML: 0.1255 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.4928
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→31.46 Å
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Refine LS restraints |
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LS refinement shell |
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