+Open data
-Basic information
Entry | Database: PDB / ID: 5c9n | ||||||
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Title | Crystal structure of GEMC1 coiled-coil domain | ||||||
Components | Geminin coiled-coil domain-containing protein 1 | ||||||
Keywords | CELL CYCLE / Geminin Idas coiled coil DNA replication license | ||||||
Function / homology | Geminin coiled-coil domain-containing protein 1 / cell cycle / negative regulation of DNA replication / negative regulation of cell cycle / cilium assembly / DNA replication initiation / chromatin binding / nucleus / Geminin coiled-coil domain-containing protein 1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Caillat, C. / Perrakis, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: The structure of the GemC1 coiled coil and its interaction with the Geminin family of coiled-coil proteins. Authors: Caillat, C. / Fish, A. / Pefani, D.E. / Taraviras, S. / Lygerou, Z. / Perrakis, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c9n.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c9n.ent.gz | 54.3 KB | Display | PDB format |
PDBx/mmJSON format | 5c9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/5c9n ftp://data.pdbj.org/pub/pdb/validation_reports/c9/5c9n | HTTPS FTP |
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-Related structure data
Related structure data | 1uiiS 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 | Mass: 10062.223 Da / Num. of mol.: 2 / Fragment: UNP residues 64-148 / Mutation: L123E, L130E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GMNC, GEMC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6NCL1 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Hepes buffer pH 7.5, 7% Ethanol, 10% 2-Methyl-2,4-pentanediol (MPD) 0.01 M Ethylene-diamine-tetra-acetic acid disodium salt dihydrate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→53.8 Å / Num. obs: 15376 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UII Resolution: 2.2→53.78 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.945 / SU B: 11.959 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.241 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→53.78 Å
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Refine LS restraints |
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