[English] 日本語
Yorodumi- PDB-4c63: ULTRA HIGH RESOLUTION DICKERSON-DREW DODECAMER B-DNA WITH 5- METH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c63 | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | ULTRA HIGH RESOLUTION DICKERSON-DREW DODECAMER B-DNA WITH 5- METHYLCYSTOSINE MODIFICATION | ||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / CYTOSINE MODIFICATION | Function / homology | DNA / DNA (> 10) | Function and homology information Biological species | SYNTHETIC CONSTRUCT (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | Authors | Mcdonough, M. / El-Sagheer, A.H. / Brown, T. / Schofield, C.J. | Citation | Journal: Chem. Commun. (Camb.) / Year: 2014 | Title: Structural insights into how 5-hydroxymethylation influences transcription factor binding. Authors: Lercher, L. / McDonough, M.A. / El-Sagheer, A.H. / Thalhammer, A. / Kriaucionis, S. / Brown, T. / Schofield, C.J. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4c63.cif.gz | 41.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4c63.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 4c63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c63_validation.pdf.gz | 381.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4c63_full_validation.pdf.gz | 386.9 KB | Display | |
Data in XML | 4c63_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 4c63_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/4c63 ftp://data.pdbj.org/pub/pdb/validation_reports/c6/4c63 | HTTPS FTP |
-Related structure data
Related structure data | 4c5xC 4c64C 1bnaS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 3677.419 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: 5-METHYL CYTOSINE AT POSITION C9 STRAND A AND C21 STRAND B, DICKERSON-DREW SEQUENCE DODECAMER Source: (synth.) SYNTHETIC CONSTRUCT (others) #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 Details: 40% MPD, SPERMINE, MAGNESIUM CHLORIDE, SODIUM CACODYLATE PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 6, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→25.34 Å / Num. obs: 16355 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Biso Wilson estimate: 19.15 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 2.3 / % possible all: 93.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BNA Resolution: 1.32→25.335 Å / SU ML: 0.14 / σ(F): 0 / Phase error: 18.37 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.29 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.41 Å2 / ksol: 0.506 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.89 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.32→25.335 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|