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- PDB-382d: HYDRATION AND RECOGNITION OF METHYLATED CPG STEPS IN DNA. -

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Basic information

Entry
Database: PDB / ID: 382d
TitleHYDRATION AND RECOGNITION OF METHYLATED CPG STEPS IN DNA.
ComponentsDNA (5'-D(*CP*CP*GP*CP*CP*GP*GP*CP*GP*G)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLECEMENT / Resolution: 2.2 Å
AuthorsMayer-Jung, C. / Moras, D. / Timsit, Y.
CitationJournal: EMBO J. / Year: 1998
Title: Hydration and recognition of methylated CpG steps in DNA.
Authors: Mayer-Jung, C. / Moras, D. / Timsit, Y.
History
DepositionMar 2, 1998Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Dec 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Advisory / Derived calculations / Refinement description
Category: pdbx_initial_refinement_model / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*GP*CP*CP*GP*GP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,0712
Polymers3,0471
Non-polymers241
Water68538
1
A: DNA (5'-D(*CP*CP*GP*CP*CP*GP*GP*CP*GP*G)-3')
hetero molecules

A: DNA (5'-D(*CP*CP*GP*CP*CP*GP*GP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1434
Polymers6,0942
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)41.500, 41.500, 57.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Cell settinghexagonal
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-19-

HOH

21A-30-

HOH

31A-31-

HOH

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Components

#1: DNA chain DNA (5'-D(*CP*CP*GP*CP*CP*GP*GP*CP*GP*G)-3')


Mass: 3046.980 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growpH: 6 / Details: pH 6.00
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3SPERMINE11
4MGCL211
5MPD12
Crystal grow
*PLUS
Temperature: 16 ℃ / 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
30.5 mMspermine1reservoir
47 mMmagnesium acetate1reservoir
530 %1reservoir

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 1, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 1510 / % possible obs: 88.9 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.056
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 15 Å / % possible obs: 88.9 % / Observed criterion σ(I): 1 / Redundancy: 4.3 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLORmodel building
X-PLOR3.851refinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLECEMENT
Starting model: STANDARD A-DNA

Resolution: 2.2→7 Å / σ(F): 2
RfactorNum. reflection
Rwork0.197 -
obs0.197 1448
all-1510
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 7 32 241
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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