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- PDB-160d: HIGH RESOLUTION CRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCCGGCCG... -

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Basic information

Entry
Database: PDB / ID: 160d
TitleHIGH RESOLUTION CRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCCGGCCGGG): NOVEL INTERMOLECULAR BASE-PAIRED G*(G.C) TRIPLETS
ComponentsDNA (5'-D(*CP*CP*CP*GP*GP*CP*CP*GP*GP*G)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsRamakrishnan, B. / Sundaralingam, M.
CitationJournal: J.Mol.Biol. / Year: 1993
Title: High resolution crystal structure of the A-DNA decamer d(CCCGGCCGGG). Novel intermolecular base-paired G*(G.C) triplets.
Authors: Ramakrishnan, B. / Sundaralingam, M.
History
DepositionFeb 10, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0May 18, 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,0942
Polymers6,0942
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.880, 44.600, 46.970
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*CP*CP*GP*GP*CP*CP*GP*GP*G)-3')


Mass: 3046.980 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4SPERMINE_HCL11
5WATER12
6MPD12

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→8 Å / Num. obs: 6033 / Observed criterion σ(I): 2.5
Reflection
*PLUS
% possible obs: 93 % / Observed criterion σ(I): 2.5 / Num. measured all: 26000 / Rmerge(I) obs: 0.031

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.65→8 Å / σ(I): 2.5 /
RfactorNum. reflection
obs0.185 6033
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 103 507
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 8 Å / Num. reflection obs: 6033 / σ(F): 2.5 / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d

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