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- PDB-383d: Hydration and recognition of methylated CPG steps in DNA -

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Basic information

Entry
Database: PDB / ID: 383d
TitleHydration and recognition of methylated CPG steps in DNA
ComponentsDNA (5'-D(*CP*(5CM)P*GP*CP*(5CM)P*GP*GP*(5CM)P*GP*G)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / MODIFIED DEOXYRIBONUCLEIC ACID
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: NDB / Processing site: NDB
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 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(*CP*(5CM)P*GP*CP*(5CM)P*GP*GP*(5CM)P*GP*G)-3')
B: DNA (5'-D(*CP*(5CM)P*GP*CP*(5CM)P*GP*GP*(5CM)P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2023
Polymers6,1782
Non-polymers241
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.900, 45.300, 46.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 3089.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
References: NDB: ADJB110
#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.: 87 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.85 %
Crystal growpH: 6 / Details: MPD, SPERMINE, MGCL2, pH 6.00
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3SPERMINE11
4MGCL211
Crystal grow
*PLUS
Temperature: 20 ℃ / 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
30.4 mMspermine1reservoir
44 mMmagnesium acetate1reservoir
535 %MPD1reservoir

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Data collection

DiffractionMean temperature: 270 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1995 / Details: DOUBLE MIRRORS
RadiationMonochromator: MIRROR + CHANNEL 4 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 5804 / % possible obs: 94.4 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.038
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / % possible obs: 94.4 % / Observed criterion σ(I): 1 / Redundancy: 4.6 %

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Processing

Software
NameVersionClassification
XDSdata scaling
AUTOMARdata reduction
X-PLORmodel building
X-PLOR3.851refinement
XDSdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ISOMORPHOUS A-DNA

Resolution: 1.7→7 Å / σ(F): 2
RfactorNum. reflection
Rwork0.196 -
obs0.196 4973
all-5804
Refinement stepCycle: LAST / Resolution: 1.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 13 81 498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27
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: 1.7 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_deg27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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