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- PDB-1vtd: UNUSUAL HELICAL PACKING IN CRYSTALS OF DNA BEARING A MUTATION HOT SPOT -

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Basic information

Entry
Database: PDB / ID: 1vtd
TitleUNUSUAL HELICAL PACKING IN CRYSTALS OF DNA BEARING A MUTATION HOT SPOT
Components
  • DNA (5'-D(*AP*CP*CP*GP*GP*CP*GP*CP*CP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*GP*GP*CP*GP*CP*CP*GP*GP*T)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsTimsit, Y. / Westhof, E. / Fuchs, R.P.P. / Moras, D.
Citation
Journal: Nature / Year: 1989
Title: Unusual helical packing in crystals of DNA bearing a mutation hot spot.
Authors: Timsit, Y. / Westhof, E. / Fuchs, R.P. / Moras, D.
#1: Journal: J. Mol. Biol. / Year: 1995
Title: Self-fitting and self-modifying properties of the B-DNA molecule.
Authors: Timsit, Y. / Moras, D.
#2: Journal: Nature / Year: 1991
Title: Base-pairing shift in the major groove of (CA)n tracts by B-DNA crystal structures.
Authors: Timsit, Y. / Vilbois, E. / Moras, D.
History
DepositionDec 12, 1996Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / pdbx_entity_src_syn / reflns
Item: _entity.src_method / _reflns.d_resolution_high / _reflns.d_resolution_low
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Dec 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*CP*CP*GP*GP*CP*GP*CP*CP*AP*CP*A)-3')
B: DNA (5'-D(*TP*GP*TP*GP*GP*CP*GP*CP*CP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)7,3282
Polymers7,3282
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-6 kcal/mol
Surface area4650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.900, 65.900, 47.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*GP*TP*GP*GP*CP*GP*CP*CP*GP*GP*T)-3')


Mass: 3710.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.1 / Details: pH 6.10, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12WATER1311
25CACODYLATE1614
38SPERMINE1917
411MG ACETATE112110
514WATER115213
617MPD118216

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Data collection

DiffractionMean temperature: 273 K
DetectorType: NICOLET / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→10 Å / Num. obs: 1584 / Observed criterion σ(F): 1

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.8→10 Å / σ(I): 3 /
RfactorNum. reflection
obs0.153 1101
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 0 486

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