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- PDB-119d: CRYSTAL AND MOLECULAR STRUCTURE OF D(CGTAGATCTACG) AT 2.25 ANGSTR... -

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Basic information

Entry
Database: PDB / ID: 119d
TitleCRYSTAL AND MOLECULAR STRUCTURE OF D(CGTAGATCTACG) AT 2.25 ANGSTROMS RESOLUTION
ComponentsDNA (5'-D(*CP*GP*TP*AP*GP*AP*TP*CP*TP*AP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsLeonard, G.A. / Hunter, W.N.
CitationJournal: J.Mol.Biol. / Year: 1993
Title: Crystal and molecular structure of d(CGTAGATCTACG) at 2.25 A resolution.
Authors: Leonard, G.A. / Hunter, W.N.
History
DepositionApr 14, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 15, 1993Provider: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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*TP*AP*GP*AP*TP*CP*TP*AP*CP*G)-3')
B: DNA (5'-D(*CP*GP*TP*AP*GP*AP*TP*CP*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3493
Polymers7,3252
Non-polymers241
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.840, 35.360, 25.350
Angle α, β, γ (deg.)90.00, 92.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-25-

MG

21A-91-

HOH

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Components

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


Mass: 3662.404 Da / Num. of mol.: 2 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2HEXANE-1,6-DIOL1,6-Hexanediol11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6WATER12
7HEXANE-1,6-DIOL1,6-Hexanediol12

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418
DetectorType: SYNTEX / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. all: 7266 / Num. obs: 3982 / Rsym value: 0.04
Reflection
*PLUS
Highest resolution: 2.2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.04

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.25→7 Å / σ(F): 2 /
RfactorNum. reflection
obs0.138 2120
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.25→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 1 137 624
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_d0.011
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.011
X-RAY DIFFRACTIONn_phos_bond_d0.026
X-RAY DIFFRACTIONn_phos_bond_angle_d0.021
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: 2.25 Å / Lowest resolution: 7 Å / Num. reflection obs: 2120 / σ(F): 2 / Rfactor obs: 0.138
Solvent computation
*PLUS
Displacement parameters
*PLUS

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