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Yorodumi- PDB-5dsb: Crystal structure of Holliday junctions stabilized by 5-hydroxyme... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dsb | ||||||||||||||||||||||||||||
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Title | Crystal structure of Holliday junctions stabilized by 5-hydroxymethylcytosine in GCC junction core | ||||||||||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Holliday junction / 5-hydroxymethylcytosine | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4959 Å | Authors | Vander Zanden, C.M. / Rowe, R.K. / Broad, A.J. / Ho, P.S. | Funding support | United States, 1items |
Citation | Journal: Biochemistry / Year: 2016 | Title: Effect of Hydroxymethylcytosine on the Structure and Stability of Holliday Junctions. Authors: Vander Zanden, C.M. / Rowe, R.K. / Broad, A.J. / Robertson, A.B. / 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 | 5dsb.cif.gz | 25 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dsb.ent.gz | 15.4 KB | Display | PDB format |
PDBx/mmJSON format | 5dsb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dsb_validation.pdf.gz | 388 KB | Display | wwPDB validaton report |
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Full document | 5dsb_full_validation.pdf.gz | 391.8 KB | Display | |
Data in XML | 5dsb_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | 5dsb_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/5dsb ftp://data.pdbj.org/pub/pdb/validation_reports/ds/5dsb | HTTPS FTP |
-Related structure data
Related structure data | 5dsaC 1p4yS S: Starting model for refinement 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
#1: DNA chain | Mass: 3077.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-CA / | #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: 2.35 Å3/Da / Density % sol: 47.64 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.78 mM DNA, 0.8 mM Spermine, 5 mM CaCl2, 25 mM sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 28, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rigaku collimator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4959→50 Å / Num. obs: 9346 / % possible obs: 99.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.52 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.036 / Rrim(I) all: 0.123 / Χ2: 6.127 / Net I/av σ(I): 50.444 / Net I/σ(I): 14.9 / Num. measured all: 62380 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1p4y Resolution: 1.4959→35.335 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.07 / 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 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 40.62 Å2 / Biso mean: 25.3288 Å2 / Biso min: 12.81 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4959→35.335 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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