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Yorodumi- PDB-1p4z: Effect of Sequence on the Conformational Geometry of DNA Holliday... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p4z | ||||||||||||||||||
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Title | Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / B-DNA / Double Helix | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | Authors | Hays, F.A. / Vargason, J.M. / Ho, P.S. | Citation | Journal: Biochemistry / Year: 2003 | Title: Effect of Sequence on the Conformation of DNA Holliday Junctions Authors: Hays, F.A. / Vargason, J.M. / 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 | 1p4z.cif.gz | 16.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p4z.ent.gz | 10.5 KB | Display | PDB format |
PDBx/mmJSON format | 1p4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p4z_validation.pdf.gz | 378.7 KB | Display | wwPDB validaton report |
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Full document | 1p4z_full_validation.pdf.gz | 379.2 KB | Display | |
Data in XML | 1p4z_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 1p4z_validation.cif.gz | 4.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/1p4z ftp://data.pdbj.org/pub/pdb/validation_reports/p4/1p4z | HTTPS FTP |
-Related 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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Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ONE CHAIN. GENERATION OF THE DOUBLE HELIX CAN BE PERFORMED WITH THE FOLLOWING: matrix= (0.50000 0.86603 0.00000 ) (0.86603 -0.50000 0.00000 ) (0.00000 0.00000 -1.00000 ) translation= (16.68855 -28.90537 14.61163) |
-Components
#1: DNA chain | Mass: 3045.004 Da / Num. of mol.: 1 / 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, FOR SUBSEQUENT HPLC ...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, FOR SUBSEQUENT HPLC PURIFICATION, THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN. | ||
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#2: Chemical | #3: 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: 1.87 Å3/Da / Density % sol: 33.78 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: 0.6mM DNA, 5mM TRIS(HCl), 25mM Ca-Acetate, 7% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 18, 2002 / Details: BENT CONICAL SI-MIRROR (RH COATING) |
Radiation | Monochromator: BENT GE(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→17.47 Å / Num. obs: 2143 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 3.6 Å2 / Rmerge(I) obs: 0.039 |
Reflection shell | Resolution: 2→2.13 Å / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 2.38 / % possible all: 74.6 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å / Num. obs: 2143 / % possible obs: 94.6 % / Rmerge(I) obs: 0.048 / Num. measured all: 32690 |
Reflection shell | *PLUS % possible obs: 53.2 % / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNPUBLISHED RESULTS OF STRUCTURE WITH ISOMORPHOUS UNIT CELL DIMENSIONS Resolution: 2→17.47 Å / Rfactor Rfree error: 0.019 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 7.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→17.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.236 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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