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- PDB-251d: SINGLE CRYSTAL AND MOLECULAR STRUCTURE OF D(CTCGAG) -

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Basic information

Entry
Database: PDB / ID: 251d
TitleSINGLE CRYSTAL AND MOLECULAR STRUCTURE OF D(CTCGAG)
ComponentsDNA (5'-D(*CP*TP*CP*GP*AP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / A-DNA LIKE CONFORMATION AT TERMINI
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsWahl, M.C. / Rao, S.T. / Sundaralingam, M.
CitationJournal: Biophys.J. / Year: 1996
Title: Crystal structure of the B-DNA hexamer d(CTCGAG): model for an A-to-B transition.
Authors: Wahl, M.C. / Rao, S.T. / Sundaralingam, M.
History
DepositionMar 1, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Jun 27, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,8091
Polymers1,8091
Non-polymers00
Water57632
1
A: DNA (5'-D(*CP*TP*CP*GP*AP*G)-3')

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


Theoretical massNumber of molelcules
Total (without water)3,6182
Polymers3,6182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)40.140, 40.140, 44.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE_HCL11
5NA CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMoligonucleotide1drop
25 mM1dropMgCl2
31 mMspermine tetrahydrochloride1drop
430 mMsodium cacodylate1drop
55 %MPD1drop
640 %MPD1reservoir
71

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 10, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 1547 / % possible obs: 83 % / Observed criterion σ(F): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.0499
Reflection
*PLUS
Highest resolution: 1.9 Å / % possible obs: 83 %

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Processing

Software
NameVersionClassification
X-PLORrefinement
XENGENV. 2.0data reduction
RefinementResolution: 1.9→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.186 -
obs0.186 1547
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 0 32 152
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg2.9
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): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.9

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