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- PDB-133d: THE CRYSTAL STRUCTURE OF N4-METHYLCYTOSINE.GUANOSIN BASE-PAIRS IN... -

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Basic information

Entry
Database: PDB / ID: 133d
TitleTHE CRYSTAL STRUCTURE OF N4-METHYLCYTOSINE.GUANOSIN BASE-PAIRS IN THE SYNTHETIC HEXANUCLEOTIDE D(CGCGM(4)CG)
ComponentsDNA (5'-D(*CP*GP*CP*GP*(C34)P*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsCervi, A.R. / Guy, A. / Leonard, G.A. / Teoule, R. / Hunter, W.N.
CitationJournal: Nucleic Acids Res. / Year: 1993
Title: The crystal structure of N4-methylcytosine.guanosine base-pairs in the synthetic hexanucleotide d(CGCGm4CG).
Authors: Cervi, A.R. / Guy, A. / Leonard, G.A. / Teoule, R. / Hunter, W.N.
History
DepositionJul 29, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 15, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*(C34)P*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*(C34)P*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6482
Polymers3,6482
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.980, 30.770, 44.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*GP*(C34)P*G)-3')


Mass: 1824.232 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.7 Å3/Da / Density % sol: 27.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6WATER12
7MPD12

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU AFC-5 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.5 Å / Num. obs: 2994
Reflection
*PLUS
Highest resolution: 1.5 Å / Observed criterion σ(F): 7

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Processing

Software
NameClassification
NUCLSQrefinement
X-PLORrefinement
RefinementResolution: 1.8→8 Å / σ(F): 1 /
RfactorNum. reflection
obs0.189 1495
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 2 49 291
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.019
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.025
X-RAY DIFFRACTIONn_phos_bond_d0.028
X-RAY DIFFRACTIONn_phos_bond_angle_d0.029
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 1495 / σ(F): 1 / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS

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