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Yorodumi- PDB-5cjy: Crystal structure of a B-form DNA duplex containing 5-hydroxylmet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cjy | ||||||||||||||||||||
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Title | Crystal structure of a B-form DNA duplex containing 5-hydroxylmethylcytidine | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / DNA duplex / B-form / 5-hydroxylmethylcytidine | Function / homology | DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | Authors | Sheng, J. | Citation | Journal: To Be Published | Title: Crystal structure of a B-form DNA duplex containing 5-hydroxylmethylcytidine Authors: Sheng, J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cjy.cif.gz | 42.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cjy.ent.gz | 28.8 KB | Display | PDB format |
PDBx/mmJSON format | 5cjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/5cjy ftp://data.pdbj.org/pub/pdb/validation_reports/cj/5cjy | HTTPS FTP |
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-Related structure data
Related structure data | 1bnaS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: DC / Beg label comp-ID: DC / End auth comp-ID: DG / End label comp-ID: DG / Refine code: 0 / Label seq-ID: 1 - 12
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-Components
#1: DNA chain | Mass: 3693.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% MPD, 40 mM Na cacodylate pH 7.0, 12 mM spermine tetra-HCl, 12mM KCl and 80 mM NaCl |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2010 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 10064 / % possible obs: 88.6 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 59 |
Reflection shell | Resolution: 1.55→1.62 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 7.15 / % possible all: 63.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BNA Resolution: 1.55→34.5 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.188 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.92 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→34.5 Å
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Refine LS restraints |
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