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- PDB-317d: STRUCTURE OF D(CCTAGGG): COMPARISON WITH NINE ISOMORPHOUS OCTAMER... -

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Basic information

Entry
Database: PDB / ID: 317d
TitleSTRUCTURE OF D(CCTAGGG): COMPARISON WITH NINE ISOMORPHOUS OCTAMER SEQUENCES REVEALS FOUR DISTINCT PATTERNS OF SEQUENCE-DEPENDENT INTERMOLECULAR INTERACTIONS
ComponentsDNA (5'-D(*CP*CP*CP*TP*AP*GP*GP*G)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsTippin, D.B. / Sundaralingam, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of d(CCCTAGGG): comparison with nine isomorphous octamer sequences reveals four distinct patterns of sequence-dependent intermolecular interactions.
Authors: Tippin, D.B. / Sundaralingam, M.
History
DepositionMar 17, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0May 22, 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,4281
Polymers2,4281
Non-polymers00
Water82946
1
A: DNA (5'-D(*CP*CP*CP*TP*AP*GP*GP*G)-3')

A: DNA (5'-D(*CP*CP*CP*TP*AP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,8552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)42.220, 42.220, 24.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 2427.605 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 295.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA CACODYLATE11
3MGCL211
4SPERMINE_HCL11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 295 K / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mMsodium cacodylate1drop
220 mM1dropMgCl2
32 mMDNA1dropsingle strand concentration
41 mMspermine tetrachloride1drop
540 %(v/v)MPD1reservoir
61

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR / Date: Mar 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 1894 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.029

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Processing

Software
NameVersionClassification
X-PLORrefinement
XENGENV. 2.0data reduction
RefinementStarting model: ADH012

Resolution: 1.9→8 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.164 -
obs0.164 1533
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 46 207
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg3.51
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS

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