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- PDB-1vt5: THE CRYSTAL STRUCTURE OF D(CCCCGGGG): A NEW A-FORM VARIANT WITH A... -

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Basic information

Entry
Database: PDB / ID: 1vt5
TitleTHE CRYSTAL STRUCTURE OF D(CCCCGGGG): A NEW A-FORM VARIANT WITH AN EXTENDED BACKBONE CONFORMATION
ComponentsDNA (5'-D(*CP*CP*CP*CP*GP*GP*GP*G)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsHaran, T.E. / Shakked, Z. / Wang, A.H.-J. / Rich, A.
Citation
Journal: J.Biomol.Struct.Dyn. / Year: 1987
Title: The crystal structure of d(CCCCGGGG): a new A-form variant with an extended backbone conformation.
Authors: Haran, T.E. / Shakked, Z. / Wang, A.H. / Rich, A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Molecular structure of the octamer d(G-G-C-C-G-G-C-C): modified A-DNA.
Authors: Wang, A.H. / Fujii, S. / van Boom, J.H. / Rich, A.
History
DepositionAug 18, 1988Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: 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*CP*GP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)2,4291
Polymers2,4291
Non-polymers00
Water00
1
A: DNA (5'-D(*CP*CP*CP*CP*GP*GP*GP*G)-3')

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


Theoretical massNumber of molelcules
Total (without water)4,8572
Polymers4,8572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area860 Å2
ΔGint-4 kcal/mol
Surface area3110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.360, 43.360, 24.830
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*CP*GP*GP*GP*G)-3')


Mass: 2428.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHESIZED DNA

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growpH: 7 / Details: MPD, Sodium Cacodylate, spermine, MgCl2, pH 7.00
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12WATER1311
25MPD1614
38NA CACODYLATE1917
411SPERMINE112110
514MGCL2115113
617WATER118216
720MPD121219

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12881
21
Diffraction source
SourceIDWavelength
SEALED TUBE11.5418
ROTATING ANODE21.5418
Detector
TypeIDDetector
NICOLET P31DIFFRACTOMETER
SIEMENS-NICOLET2AREA DETECTOR
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21
ReflectionHighest resolution: 2.25 Å

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Processing

SoftwareName: CORELS / Classification: refinement
RefinementResolution: 2.25→8 Å
Details: REFERENCE 2 REPORTED A CELL OF 42.10, 42.10, 25.10 WITH SPACE GROUP OF P 43 21 2. THIS HAS SINCE BEEN CHANGED TO THE PRESENT CELL.
RfactorNum. reflection
Rwork0.24 -
obs0.24 1018
Refine Biso Class: ALL ATOMS / Details: TR / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 2.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 0 161

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