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- PDB-1v9g: Neutron Crystallographic analysis of the Z-DNA hexamer CGCGCG -

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Basic information

Entry
Database: PDB / ID: 1v9g
TitleNeutron Crystallographic analysis of the Z-DNA hexamer CGCGCG
Components5'-D(*CP*GP*CP*GP*CP*G)-3'
KeywordsDNA / Z-DNA / HYDROGEN / HYDRATION / H/D EXCHANGE / NEUTRON
Function / homologyDEUTERATED WATER / N,N'-BIS(3-AMMONIOPROPYL)BUTANE-1,4-DIAMINIUM / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChatake, T. / Tanaka, I. / 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
DepositionJan 26, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 21, 2013Group: Derived calculations / Other
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Jun 20, 2018Group: Data collection / Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.6Nov 28, 2018Group: Data collection / Source and taxonomy
Category: diffrn_detector / diffrn_source / pdbx_entity_src_syn
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_beamline ..._diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.7Dec 5, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_scattering_type
Revision 1.8Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,8373
Polymers3,6202
Non-polymers2161
Water79344
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 5'-D(*CP*GP*CP*GP*CP*G)-3'


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Z-DNA duplex / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SPW / N,N'-BIS(3-AMMONIOPROPYL)BUTANE-1,4-DIAMINIUM / SPERMINE (FULLY DEUTERATED FORM)


Mass: 216.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20N4
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.35 Å3/Da / Density % sol: 7.98 %
Crystal growTemperature: 328 K / Method: small tubes / pH: 7
Details: MPD, sodium cacodylate, magnesium chloride, spermine, pH 7.0, SMALL TUBES, temperature 328K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3MgCl211
4spermine11
5MPD12
6sodium cacodylate12
7MgCl212

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: JRR-3M / Beamline: 1G-A / Wavelength: 2.88 Å
DetectorType: BIX-3M / Detector: DIFFRACTOMETER / Date: Jun 10, 2003
RadiationMonochromator: Elastically-bent perfect silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.88 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 2627 / Num. obs: 2627 / % possible obs: 73.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 3.9 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 6.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 3.5 / Num. unique all: 142 / % possible all: 40.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IOT

1iot


Resolution: 1.8→25.05 Å / Data cutoff high absF: 3 / Data cutoff low absF: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.294 163 6.5 %RANDOM
Rwork0.222 ---
all0.256 2510 --
obs0.229 1821 72.5 %-
Solvent computationSolvent model: bulk solvent correction / Bsol: 20.1 Å2 / ksol: 0.06 e/Å3
Displacement parametersBiso mean: 12.09 Å2
Baniso -1Baniso -2Baniso -3
1-1.289 Å20 Å20 Å2
2--1.581 Å20 Å2
3----2.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.8→25.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 14 44 298
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONc_bond_d0.005
NEUTRON DIFFRACTIONc_angle_deg0.83
NEUTRON DIFFRACTIONc_dihedral_angle_d0.43
NEUTRON DIFFRACTIONc_improper_angle_d0.82
LS refinement shell

Refine-ID: NEUTRON DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.910.425194.80.29320656.7
1.91-2.060.322200.28561.7
2.06-2.270.327290.26771.4
2.27-2.60.283240.2576.3
2.6-3.270.312330.19180.7
3.27-500.234380.16286

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