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- PDB-1woe: X-ray structure of a Z-DNA hexamer d(CGCGCG) -

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Basic information

Entry
Database: PDB / ID: 1woe
TitleX-ray structure of a Z-DNA hexamer d(CGCGCG)
ComponentsZ-DNA hexamer
KeywordsDNA / Z-DNA / heavy water / spermine
Function / homologyDEUTERATED WATER / SPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChatake, T. / Tanaka, I. / Umino, H. / Arai, S. / Niimura, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: The hydration structure of a Z-DNA hexameric duplex determined by a neutron diffraction technique.
Authors: Chatake, T. / Tanaka, I. / Umino, H. / Arai, S. / Niimura, N.
History
DepositionAug 15, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Z-DNA hexamer
B: Z-DNA hexamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8233
Polymers3,6202
Non-polymers2021
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)18.460, 30.760, 43.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain Z-DNA hexamer


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: D2O

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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: 1.69 Å3/Da / Density % sol: 27.35 %
Crystal growMethod: slow cooling / pH: 6.6 / Details: pH 6.6, SLOW COOLING
Components of the solutionsName: spermine

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Sep 2, 2002 / Details: monochromator
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 4998 / Num. obs: 4998 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.096
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 12.6 / % possible all: 95.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.206 427 random
Rwork0.176 --
all0.18 4481 -
obs0.178 4054 -
Displacement parametersBiso mean: 12.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å20 Å2
2---0.2 Å20 Å2
3---1.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.03 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 14 57 311
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d34.4
X-RAY DIFFRACTIONc_improper_angle_d0.81

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