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- PDB-240d: EFFECT OF END BASE STEPS ON DNA FORM: CRYSTAL STRUCTURE OF THE A-... -

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Basic information

Entry
Database: PDB / ID: 240d
TitleEFFECT OF END BASE STEPS ON DNA FORM: CRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCGGGCCCGG)
ComponentsDNA (5'-D(*CP*CP*GP*GP*GP*CP*CP*CP*GP*G)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / DEOXYRIBONUCLEIC ACID
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsChampion, D. / Kumar, C.S. / Ramakrishnan, B. / Gautham, N. / Viswamitra, M.A.
CitationJournal: To be Published
Title: Effect of End Base Steps on DNA Form: Crystal Structure of the A-DNA Decamer d(CCGGGCCCGG)
Authors: Champion, D. / Kumar, C.S. / Ramakrishnan, B. / Gautham, N. / Viswamitra, M.A.
History
DepositionNov 8, 1995Processing site: NDB
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,0942
Polymers6,0942
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.396, 45.515, 48.456
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*CP*GP*GP*GP*CP*CP*CP*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.: 72 / 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: 2.3 Å3/Da / Density % sol: 46.47 %

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Data collection

Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS / Detector: DIFFRACTOMETER / Date: Mar 1, 1991
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 1591 / Observed criterion σ(I): 3

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Processing

Software
NameClassification
X-PLORrefinement
SDPdata scaling
RefinementResolution: 2→8 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.19 -
obs0.19 2697
Displacement parametersBiso mean: 30.03 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 72 476
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg4.83
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d4.4
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

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