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- PDB-3wbo: Crystal Structure Analysis of the Z-DNA hexamer CGCGCG with 40 mM NaCl -

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Basic information

Entry
Database: PDB / ID: 3wbo
TitleCrystal Structure Analysis of the Z-DNA hexamer CGCGCG with 40 mM NaCl
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / DOUBLE HELIX / Z-DNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsChatake, T.
CitationJournal: J.SYNCHROTRON RADIAT. / Year: 2013
Title: Structural fluctuation observed in Z-DNA d(CGCGCG)2 in the absence of divalent metal cations and polyamines
Authors: Chatake, T.
History
DepositionMay 20, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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*GP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-5 kcal/mol
Surface area2310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.844, 30.630, 43.632
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 DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 1.65 Å3/Da / Density % sol: 25.3 %
Crystal growTemperature: 293 K / Method: slow cooling / pH: 7
Details: 2.0mM DNA, 20mM Na cacodylate, 30% 2-methyl-2,4-pentainediol, 20mM NaCl, pH 7.0, SLOW COOLING, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 13, 2008
RadiationMonochromator: Fixed exit Si (111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.98→50 Å / Num. obs: 14112 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 7.22 Å2 / Rmerge(I) obs: 0.04
Reflection shell
Resolution (Å)Diffraction-ID% possible all
0.98-1.06196.2
1.06-1.16197.3
1.16-1.33199.3
1.33-1.68199.8
1.68-50198.2

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Processing

Software
NameVersionClassification
BSSdata collection
AMoREphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.98→17.77 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.9208 / SU ML: 0.1 / σ(F): 0 / Phase error: 13.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1626 699 4.98 %RANDOM
Rwork0.1555 ---
obs0.1559 14024 97.89 %-
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.793 Å2 / ksol: 0.503 e/Å3
Displacement parametersBiso max: 28.08 Å2 / Biso mean: 9.0832 Å2 / Biso min: 4.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.7429 Å20 Å20 Å2
2--0.1247 Å2-0 Å2
3---0.6182 Å2
Refinement stepCycle: LAST / Resolution: 0.98→17.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 0 72 312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013369
X-RAY DIFFRACTIONf_angle_d2.178582
X-RAY DIFFRACTIONf_chiral_restr0.08477
X-RAY DIFFRACTIONf_plane_restr0.01620
X-RAY DIFFRACTIONf_dihedral_angle_d30.66191
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.98-1.05570.17071340.14782537267196
1.0557-1.16190.15371350.1272591272697
1.1619-1.330.13561410.12572665280699
1.33-1.67550.16161410.131927212862100
1.6755-17.77250.17111480.18072811295998

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