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- PDB-4ocb: Z-DNA dodecamer d(CGCGCGCGCGCG)2 at 0.75 A resolution solved by P-SAD -

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Basic information

Entry
Database: PDB / ID: 4ocb
TitleZ-DNA dodecamer d(CGCGCGCGCGCG)2 at 0.75 A resolution solved by P-SAD
Componentsd(CGCGCGCGCGCG)2 duplex
KeywordsDNA / Z-DNA dodecamer duplex
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.75 Å
AuthorsLuo, Z. / Dauter, M. / Dauter, Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution
Authors: Luo, Z. / Dauter, M. / Dauter, Z.
History
DepositionJan 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Feb 28, 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: d(CGCGCGCGCGCG)2 duplex


Theoretical massNumber of molelcules
Total (without water)3,6651
Polymers3,6651
Non-polymers00
Water1,44180
1
A: d(CGCGCGCGCGCG)2 duplex

A: d(CGCGCGCGCGCG)2 duplex


Theoretical massNumber of molelcules
Total (without water)7,3312
Polymers7,3312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1270 Å2
ΔGint-11 kcal/mol
Surface area4310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.484, 19.546, 31.224
Angle α, β, γ (deg.)90.00, 116.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain d(CGCGCGCGCGCG)2 duplex


Mass: 3665.368 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 31.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2:1 mixture of 1.66 mM DNA solution with the following solution: 40mM Na cacodylate pH 7.0, 12 mM spermine tetrachloride, 80 mM NaCl, 10% (v/v) MPD. The well solution contained 35% MPD., ...Details: 2:1 mixture of 1.66 mM DNA solution with the following solution: 40mM Na cacodylate pH 7.0, 12 mM spermine tetrachloride, 80 mM NaCl, 10% (v/v) MPD. The well solution contained 35% MPD., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.6199 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 0.75→30 Å / Num. all: 32210 / Num. obs: 32210 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Biso Wilson estimate: 6.9 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 84.7
Reflection shellResolution: 0.75→0.76 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1525 / Rsym value: 0.734 / % possible all: 92.2

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Processing

Software
NameClassification
NE-CATdata collection
SHELXDphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 0.75→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Parkinson
RfactorNum. reflectionSelection details
Rfree0.134 1601 Random
Rwork0.122 --
all0.122 32194 -
obs0.122 32194 -
Refinement stepCycle: LAST / Resolution: 0.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 243 0 80 323
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.05
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.029

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