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Yorodumi- PDB-2qby: Crystal structure of a heterodimer of Cdc6/Orc1 initiators bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qby | ||||||
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Title | Crystal structure of a heterodimer of Cdc6/Orc1 initiators bound to origin DNA (from S. solfataricus) | ||||||
Components |
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Keywords | REPLICATION/DNA / winged-helix domain / helix-turn-helix / AAA+ ATPase domain / protein-DNA complex / double helix / REPLICATION-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.35 Å | ||||||
Authors | Cunningham Dueber, E.L. / Corn, J.E. / Bell, S.D. / Berger, J.M. | ||||||
Citation | Journal: Science / Year: 2007 Title: Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. Authors: Dueber, E.L. / Corn, J.E. / Bell, S.D. / Berger, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qby.cif.gz | 391.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qby.ent.gz | 316.6 KB | Display | PDB format |
PDBx/mmJSON format | 2qby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qby_validation.pdf.gz | 1007.9 KB | Display | wwPDB validaton report |
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Full document | 2qby_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2qby_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 2qby_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/2qby ftp://data.pdbj.org/pub/pdb/validation_reports/qb/2qby | HTTPS FTP |
-Related structure data
Related structure data | 1fnnS 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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Details | heterodimer of Orc1-1 and Orc1-3 bound to a 33bp DNA per asymmetric unit |
-Components
-DNA chain , 2 types, 2 molecules CD
#1: DNA chain | Mass: 10200.622 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 10093.530 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Cell division control protein 6 homolog ... , 2 types, 2 molecules AB
#3: Protein | Mass: 43922.883 Da / Num. of mol.: 1 / Fragment: Residues 15-397 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: cdc6-1 / Plasmid: pSV271 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+ / References: UniProt: Q980N4 |
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#4: Protein | Mass: 43468.004 Da / Num. of mol.: 1 / Fragment: Residues 14-394 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: cdc6-3 / Plasmid: pSV271 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+ / References: UniProt: Q97WM8 |
-Non-polymers , 5 types, 11 molecules
#5: Chemical | #6: Chemical | ChemComp-K / | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.68 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: microbatch / pH: 5 Details: 25mM HEPES pH 7.5, 50mM sodium chloride, 5% glycerol, 0.5mM TCEP, 15mM spermidine, 15mM sodium cacodylate pH 5.0, 4.4% (w/v) PEG 3350 and 25mM potassium thiocyanate, microbatch, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11111, 0.979578, 0.979733, 0.987379 | |||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 20, 2006 | |||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.35→50 Å / Num. all: 24607 / Num. obs: 24287 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 119 Å2 / Net I/σ(I): 25.4 | |||||||||||||||
Reflection shell | Resolution: 3.35→3.47 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.835 / Mean I/σ(I) obs: 1.93 / Num. unique all: 2385 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: PDB entry 1FNN Resolution: 3.35→30 Å / Isotropic thermal model: ISOTROPIC GROUPED B FACTOR / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber Details: The authors state that the ANISOU lines in the pdb refer to TLS parameters, not anisotropic B factors.
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Refinement step | Cycle: LAST / Resolution: 3.35→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.35→3.48 Å
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