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- PDB-2f8w: Crystal structure of d(CACGTG)2 -

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Basic information

Entry
Database: PDB / ID: 2f8w
TitleCrystal structure of d(CACGTG)2
Components5'-D(*CP*AP*CP*GP*TP*G)-3'
KeywordsDNA / d(CACGTG) / Polyamine / Z-DNA / 1 / 3-propanediamine
Function / homology1,3-DIAMINOPROPANE / SPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsNarayana, N. / Shamala, N. / Ganesh, K.N. / Viswamitra, M.A.
Citation
Journal: Biochemistry / Year: 2006
Title: Interaction between the Z-Type DNA Duplex and 1,3-Propanediamine: Crystal Structure of d(CACGTG)2 at 1.2 A Resolution
Authors: Narayana, N. / Shamala, N. / Ganesh, K.N. / Viswamitra, M.A.
#1: Journal: Biochemistry / Year: 1991
Title: Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-resolution
Authors: Egli, M. / Williams, L.D. / Gao, Q. / Rich, A.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of d(TGCGCA)2 at 293 K: comparison of the effects of sequence and temperature
Authors: Thiyagarajan, S. / Satheesh Kumar, P. / Rajan, S.S. / Gautham, N.
#3: Journal: J.Mol.Biol. / Year: 1995
Title: Sequence-dependent microheterogeneity of Z-DNA: The crystal and molecular structures of d(CACGCG).d(CGCGTG) and d(CGCACG).d(CGTGCG)
Authors: Sadasivan, C. / Gautham, N.
#4: Journal: Nucleic Acids Res. / Year: 2004
Title: Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA)*d(TGCGCG) in two crystal forms
Authors: Thiyagarajan, S. / Rajan, S.S. / Gautham, N.
#5: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of d(TGCGCA)2 and a comparison to other DNA hexamers.
Authors: Harper, A. / Brannigan, J.A. / Buck, M. / Hewitt, L. / Lewis, R.J. / Moore, M.H. / Schneider, B.
#6: Journal: Nucleic Acids Res. / Year: 1988
Title: Structure of d(CACGTG), Z-DNA hexamer containing AT base pairs
Authors: Coll, M. / Fita, I. / Lloveras, J. / Subirana, J.A. / Bardella, F. / Huynh-Dinh, T. / Igolen, J.
History
DepositionDec 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN Ligand Z5 in the manuscript is labeled as 13D in the coordinate file.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,8954
Polymers3,6182
Non-polymers2762
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)18.420, 30.740, 43.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a duplex. The coordinates deposited will generate the biological assembly. There is no need for symmetry operations to generate the biological assembly.

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Components

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


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligonucleotide
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical ChemComp-13D / 1,3-DIAMINOPROPANE


Mass: 74.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H10N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1.71 Å3/Da / Density % sol: 28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 7.5 mM sodium cacodylate, 2.5 mM SrCl2, 2.5 mM spermine, 50% Isopropanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2SrCl211
3spermine11
4Isopropanol11
5H2O11
6sodium cacodylate12
7SrCl212
8H2O12

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SEALED TUBE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER / Date: Feb 4, 1987
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 8124 / Num. obs: 5687 / % possible obs: 70 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Rsym value: 0.042

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Processing

Software
NameVersionClassification
CAD4data collection
CAD4associated programdata reduction
X-PLORmodel building
X-PLORrefinement
CAD4data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1D48

1d48


Resolution: 1.2→6 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4 / Details: X-PLOR
RfactorNum. reflection% reflectionSelection details
Rfree0.215 93 1.5 %RANDOM
Rwork0.18 ---
all0.183 ---
obs0.183 5687 70 %-
Displacement parametersBiso mean: 14.8 Å2
Refinement stepCycle: LAST / Resolution: 1.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 19 71 330
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg3.18
X-RAY DIFFRACTIONx_dihedral_angle_deg32.14
X-RAY DIFFRACTIONx_improper_angle_deg1.32

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