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Yorodumi- PDB-1t6f: Crystal Structure of the Coiled-coil Dimerization Motif of Geminin -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t6f | ||||||
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Title | Crystal Structure of the Coiled-coil Dimerization Motif of Geminin | ||||||
Components | Geminin | ||||||
Keywords | CELL CYCLE / COILED-COIL | ||||||
Function / homology | Function and homology information DNA replication preinitiation complex assembly / Switching of origins to a post-replicative state / negative regulation of DNA-templated DNA replication / positive regulation of chromatin binding / regulation of DNA-templated DNA replication initiation / negative regulation of DNA replication / regulation of mitotic cell cycle / regulation of DNA replication / negative regulation of cell cycle / Activation of the pre-replicative complex ...DNA replication preinitiation complex assembly / Switching of origins to a post-replicative state / negative regulation of DNA-templated DNA replication / positive regulation of chromatin binding / regulation of DNA-templated DNA replication initiation / negative regulation of DNA replication / regulation of mitotic cell cycle / regulation of DNA replication / negative regulation of cell cycle / Activation of the pre-replicative complex / transcription repressor complex / Assembly of the pre-replicative complex / animal organ morphogenesis / histone deacetylase binding / transcription corepressor activity / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / chromatin binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Thepaut, M. / Maiorano, D. / Guichou, J.-F. / Auge, M.-T. / Dumas, C. / Mechali, M. / Padilla, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal Structure of the Coiled-coil Dimerization Motif of Geminin: Structural and Functional Insights on DNA Replication Regulation Authors: Thepaut, M. / Maiorano, D. / Guichou, J.-F. / Auge, M.-T. / Dumas, C. / Mechali, M. / Padilla, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t6f.cif.gz | 42 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t6f.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 1t6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/1t6f ftp://data.pdbj.org/pub/pdb/validation_reports/t6/1t6f | HTTPS FTP |
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-Related structure data
Related structure data | 1e7t S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4404.987 Da / Num. of mol.: 2 / Fragment: COILED-COIL DOMAIN / Mutation: A1T / Source method: obtained synthetically Details: The peptide was synthesized using Fmoc solid-phase peptide synthesis. The sequence of the peptide is naturally found in Homo sapiens (human). References: UniProt: O75496 #2: Water | ChemComp-HOH / | |
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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: 2.09 Å3/Da / Density % sol: 41.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG 6000, 5% MPD, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 17, 2003 / Details: osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→36.52 Å / Num. all: 13979 / Num. obs: 12978 / % possible obs: 92.8 % / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.44→1.52 Å / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E7T 1e7t Resolution: 1.47→25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.361 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.095 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.47→1.508 Å / Total num. of bins used: 20
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