+Open data
-Basic information
Entry | Database: PDB / ID: 3a4c | ||||||
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Title | Crystal structure of cdt1 C terminal domain | ||||||
Components | DNA replication factor Cdt1 | ||||||
Keywords | Cell cycle / Replication / alpha-beta structure / DNA replication / DNA-binding / Nucleus / Phosphoprotein / Proto-oncogene / Ubl conjugation | ||||||
Function / homology | Function and homology information Switching of origins to a post-replicative state / Activation of the pre-replicative complex / DNA replication preinitiation complex assembly / response to sorbitol / positive regulation of DNA-templated DNA replication / Assembly of the pre-replicative complex / Orc1 removal from chromatin / regulation of nuclear cell cycle DNA replication / negative regulation of DNA-templated DNA replication / DNA replication checkpoint signaling ...Switching of origins to a post-replicative state / Activation of the pre-replicative complex / DNA replication preinitiation complex assembly / response to sorbitol / positive regulation of DNA-templated DNA replication / Assembly of the pre-replicative complex / Orc1 removal from chromatin / regulation of nuclear cell cycle DNA replication / negative regulation of DNA-templated DNA replication / DNA replication checkpoint signaling / attachment of mitotic spindle microtubules to kinetochore / regulation of DNA-templated DNA replication initiation / negative regulation of cell cycle / DNA polymerase binding / positive regulation of DNA replication / kinetochore / mitotic cell cycle / nuclear body / chromatin binding / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.889 Å | ||||||
Authors | Cho, Y. / Lee, J.H. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Structure of the Cdt1 C-terminal domain: Conservation of the winged helix fold in replication licensing factors Authors: Khayrutdinov, B.I. / Bae, W.J. / Yun, Y.M. / Lee, J.H. / Tsuyama, T. / Kim, J.J. / Hwang, E. / Ryu, K.-S. / Cheong, H.-K. / Cheong, C. / Ko, J.-S. / Enomoto, T. / Karplus, P.A. / Guntert, P. ...Authors: Khayrutdinov, B.I. / Bae, W.J. / Yun, Y.M. / Lee, J.H. / Tsuyama, T. / Kim, J.J. / Hwang, E. / Ryu, K.-S. / Cheong, H.-K. / Cheong, C. / Ko, J.-S. / Enomoto, T. / Karplus, P.A. / Guntert, P. / Tada, S. / Jeon, Y.H. / Cho, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a4c.cif.gz | 33.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a4c.ent.gz | 23 KB | Display | PDB format |
PDBx/mmJSON format | 3a4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/3a4c ftp://data.pdbj.org/pub/pdb/validation_reports/a4/3a4c | 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: 12108.196 Da / Num. of mol.: 1 / Fragment: C terminal domain, residues 452-557 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdt1, Ris2 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8R4E9 |
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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: 2.74 Å3/Da / Density % sol: 55.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 3.8M NaCl, 100mM Sodium Citrate, 5mM DTT, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Aug 10, 2007 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.889→50 Å / Num. all: 20616 / Num. obs: 11409 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 15.2 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.064 / Net I/σ(I): 67 |
Reflection shell | Resolution: 1.889→1.97 Å / Redundancy: 15.1 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 12.1 / Num. unique all: 1122 / Rsym value: 0.334 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.889→37.169 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / σ(F): 0.29 / Phase error: 19.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.73 Å2 / ksol: 0.404 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.21 Å2 / Biso mean: 21.061 Å2 / Biso min: 3.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.889→37.169 Å
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Refine LS restraints |
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LS refinement shell |
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