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- PDB-7zqo: d(CGCGCG)2 Z-DNA AT 7150 BARS (715 MPa) -

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Basic information

Entry
Database: PDB / ID: 7zqo
Titled(CGCGCG)2 Z-DNA AT 7150 BARS (715 MPa)
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / HIGH PRESSURE / DIAMOND ANVIL CELL
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsPrange, T. / Colloc'h, N. / Girard, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Crystals / Year: 2022
Title: Behavior of B- and Z-DNA Crystals under High Hydrostatic Pressure
Authors: Prange, T. / Colloc'h, N. / Dhaussy, A.C. / Lecouvey, M. / Migianu-Griffoni, E. / Girard, E.
#1: Journal: Nucleic Acids Res / Year: 2007
Title: Adaptation of the base-paired double-helix molecular architecture to extreme pressure.
Authors: Girard, E. / Prange, T. / Dhaussy, A.C. / Migianu-Griffoni, E. / Lecouvey, M. / Chervin, J.C. / Mezouar, M. / Kahn, R. / Fourme, R.
History
DepositionMay 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
BBB: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.770, 30.870, 43.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 25.27 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 6.9
Details: 10 mg of compound dissolved in 100 microLiter of 20 % MPD cacodylate buffer + 0.01 M MgCl2

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.75003 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75003 Å / Relative weight: 1
ReflectionResolution: 1.41→25.165 Å / Num. obs: 3464 / % possible obs: 69.9 % / Redundancy: 5.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.066 / Net I/σ(I): 10.6
Reflection shellResolution: 1.41→1.44 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.45 / Num. unique obs: 255 / CC1/2: 0.88 / Rpim(I) all: 0.301 / % possible all: 66.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2ELG

2elg


Resolution: 1.8→25.165 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.446 / WRfactor Rwork: 0.329 / SU B: 3.923 / SU ML: 0.122 / Average fsc free: 0.844 / Average fsc work: 0.926 / Cross valid method: FREE R-VALUE / ESU R: 0.34 / ESU R Free: 0.245
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2831 83 4.851 %
Rwork0.2121 1628 -
all0.215 --
obs-1711 69.98 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.969 Å2
Baniso -1Baniso -2Baniso -3
1--0.366 Å20 Å2-0 Å2
2--0.149 Å2-0 Å2
3---0.217 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 0 48 288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.012268
X-RAY DIFFRACTIONr_bond_other_d0.0020.017134
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.729410
X-RAY DIFFRACTIONr_angle_other_deg0.2911.574314
X-RAY DIFFRACTIONr_chiral_restr0.1690.246
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0248
X-RAY DIFFRACTIONr_nbd_refined0.1710.287
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2460.2129
X-RAY DIFFRACTIONr_nbtor_refined0.270.282
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0950.280
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.219
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.216
X-RAY DIFFRACTIONr_nbd_other0.2140.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3250.214
X-RAY DIFFRACTIONr_scbond_it1.0061.038268
X-RAY DIFFRACTIONr_scbond_other1.0061.039268
X-RAY DIFFRACTIONr_scangle_it1.4281.554410
X-RAY DIFFRACTIONr_scangle_other1.4261.553411
X-RAY DIFFRACTIONr_lrange_it3.31611.19437
X-RAY DIFFRACTIONr_lrange_other3.15311.013434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.26890.24387X-RAY DIFFRACTION57.485
1.847-1.8970.2750.26493X-RAY DIFFRACTION56.9767
1.897-1.9520.22950.22786X-RAY DIFFRACTION54.8193
1.952-2.0110.42420.25391X-RAY DIFFRACTION58.125
2.011-2.0770.37720.19790X-RAY DIFFRACTION58.5987
2.077-2.1490.26880.26779X-RAY DIFFRACTION57.2368
2.149-2.230.24310.20489X-RAY DIFFRACTION58.0645
2.23-2.320.59420.2480X-RAY DIFFRACTION64.0625
2.32-2.4220.26380.15979X-RAY DIFFRACTION63.0435
2.422-2.5390.71310.24493X-RAY DIFFRACTION64.3836
2.539-2.6750.22430.21882X-RAY DIFFRACTION72.6496
2.675-2.8360.39930.19379X-RAY DIFFRACTION73.2143
2.836-3.0290.39480.16582X-RAY DIFFRACTION75.6303
3.029-3.2670.44160.19284X-RAY DIFFRACTION89.1089
3.267-3.5730.2490.218102X-RAY DIFFRACTION99.1071
3.573-3.9850.30510.23889X-RAY DIFFRACTION100
3.985-4.5820.5520.14376X-RAY DIFFRACTION100
4.582-5.5660.18940.17469X-RAY DIFFRACTION100
5.566-7.6860.54620.21659X-RAY DIFFRACTION100
7.686-100.25520.24438X-RAY DIFFRACTION100

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