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- PDB-329d: EFFECT OF CYTOSINE METHYLATION ON DNA-DNA RECOGNITION AT CPG STEPS -

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Basic information

Entry
Database: PDB / ID: 329d
TitleEFFECT OF CYTOSINE METHYLATION ON DNA-DNA RECOGNITION AT CPG STEPS
Components
  • DNA (5'-D(*AP*CP*CP*GP*CP*(5CM)P*GP*GP*CP*GP*CP*C)-3')
  • DNA (5'-D(*GP*GP*CP*GP*CP*(5CM)P*GP*GP*CP*GP*GP*T)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMayer-Jung, C. / Moras, D. / Timsit, Y.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Effect of cytosine methylation on DNA-DNA recognition at CpG steps.
Authors: Mayer-Jung, C. / Moras, D. / Timsit, Y.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Self-Fitting and Self-Modifying Properties of the B-DNA Molecule
Authors: Timsit, Y. / Moras, D.
#2: Journal: Nature / Year: 1991
Title: Base-Pairing Shift in the Major Groove of (CA)n Tracts by B-DNA Crystal Structures
Authors: Timsit, Y. / Vilbois, E. / Moras, D.
History
DepositionApr 29, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 30, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*CP*CP*GP*CP*(5CM)P*GP*GP*CP*GP*CP*C)-3')
B: DNA (5'-D(*GP*GP*CP*GP*CP*(5CM)P*GP*GP*CP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)7,3582
Polymers7,3582
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.530, 65.530, 46.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: DNA chain DNA (5'-D(*AP*CP*CP*GP*CP*(5CM)P*GP*GP*CP*GP*CP*C)-3')


Mass: 3623.372 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#2: DNA chain DNA (5'-D(*GP*GP*CP*GP*CP*(5CM)P*GP*GP*CP*GP*GP*T)-3')


Mass: 3734.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growMethod: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3CACODYLATECacodylic acid11
4SPERMINE11
5MG ACETATE11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 mMdodecamer duplex solution1drop
250 mMsodium cacodylate1reservoir
310 mMmagnesium acetate1reservoir
430 %MPD1reservoir
51
61
71

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Data collection

DiffractionMean temperature: 273 K
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→19.5 Å / Num. obs: 1789 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 8.2 % / Rmerge(I) obs: 0.054

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BDL035

Resolution: 2.7→8 Å / Data cutoff high absF: 1000 / Data cutoff low absF: 0.001 / σ(F): 2 /
RfactorNum. reflection
Rwork0.191 -
obs0.191 1626
Displacement parametersBiso mean: 36 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 2 41 529
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.43
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.96
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA.PARAMDNA.TOP
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.025
X-RAY DIFFRACTIONx_angle_d0.050.028
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.96

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