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Yorodumi- PDB-1ksy: Crystal Structures of Two Intermediates in the Assembly of the Pa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ksy | ||||||
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Title | Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex | ||||||
Components |
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Keywords | REPLICATION/DNA / PAPILLOMAVIRUS / DNA-BINDING DOMAIN / REPLICATION / INITIATOR PROTEIN / HELICASE / REPLICATION-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA helicase activity / DNA helicase / DNA replication / host cell nucleus / ATP hydrolysis activity / DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Bovine papillomavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | ||||||
Authors | Enemark, E.J. / Stenlund, A. / Joshua-Tor, L. | ||||||
Citation | Journal: EMBO J. / Year: 2002 Title: Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex. Authors: Enemark, E.J. / Stenlund, A. / Joshua-Tor, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ksy.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ksy.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ksy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/1ksy ftp://data.pdbj.org/pub/pdb/validation_reports/ks/1ksy | HTTPS FTP |
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-Related structure data
Related structure data | 1ksxC 1f08S C: citing same article (ref.) 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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2 |
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Unit cell |
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Details | E1 dimerization occurs upon binding to the adjacent sites of the target DNA sequence. |
-Components
#1: DNA chain | Mass: 6435.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 5'-ATAATTGTTGTTAACAATAAT-3' #2: DNA chain | | Mass: 6444.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5'-ATTATTGTTAACAACAATTAT-3' #3: Protein | Mass: 17565.467 Da / Num. of mol.: 3 / Fragment: DNA Binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bovine papillomavirus / Plasmid: PET11CGST / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03116 #4: 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: 3.8 Å3/Da / Density % sol: 67.66 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MgSO4, spermine tetrahydrochloride, ethylene glycol, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 14, 2000 / Details: mirrors |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→50 Å / Num. obs: 20851 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 3.05→3.16 Å / Redundancy: 3.59 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2091 / % possible all: 99.6 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 72557 |
Reflection shell | *PLUS % possible obs: 99.6 % / Num. unique obs: 2091 / Num. measured obs: 6981 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F08 Resolution: 3.05→35.53 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 244686.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 17.6956 Å2 / ksol: 0.261155 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.05→35.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.05→3.24 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor obs: 0.2805 / Rfactor Rfree: 0.3172 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.48 |