+Open data
-Basic information
Entry | Database: PDB / ID: 1zfb | ||||||||||||||||||
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Title | GGC Duplex B-DNA | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Crystallographic Screen / DNA Structure / Holliday Junction / Molecular Structure | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | Authors | Hays, F.A. / Teegarden, A.T. / Jones, Z.J.R. / Harms, M. / Raup, D. / Watson, J. / Cavaliere, E. / Ho, P.S. | Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 | Title: How sequence defines structure: a crystallographic map of DNA structure and conformation. Authors: Hays, F.A. / Teegarden, A. / Jones, Z.J. / Harms, M. / Raup, D. / Watson, J. / Cavaliere, E. / Ho, P.S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zfb.cif.gz | 22.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zfb.ent.gz | 15.1 KB | Display | PDB format |
PDBx/mmJSON format | 1zfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zfb_validation.pdf.gz | 382.6 KB | Display | wwPDB validaton report |
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Full document | 1zfb_full_validation.pdf.gz | 386.3 KB | Display | |
Data in XML | 1zfb_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 1zfb_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/1zfb ftp://data.pdbj.org/pub/pdb/validation_reports/zf/1zfb | HTTPS FTP |
-Related structure data
Related structure data | 1zewC 1zexC 1zeyC 1zezC 1zf0C 1zf1C 1zf2C 1zf3C 1zf4C 1zf5C 1zf6C 1zf7C 1zf8C 1zf9C 1zfaC 1zfcC 1zfeC 1zffC 1zfgC 1zfhC 1zfmC C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3046.980 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'-TERMINAL NUCLEOTIDE THEN DEPROTECTED BY ...Details: DNA WAS SYNTHESIZED ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER USING PHOSPHORAMIDITE CHEMISTRY, WITH THE TRITYL-PROTECTING GROUP LEFT INTACT AT THE 5'-TERMINAL NUCLEOTIDE THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN. #2: Chemical | #3: 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: 2.04 Å3/Da / Density % sol: 39.6 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / pH: 7 Details: Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.542 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 24, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→99 Å / Num. obs: 5484 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 6 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.65→1.71 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.8 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ndb entry BD0015 Resolution: 1.65→16.35 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 30238.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: STRUCTURE IS NOT FULLY REFINED. REFER TO CITATION ABOVE FOR DETAILS.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 132.057 Å2 / ksol: 0.671 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→16.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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