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- PDB-8a71: Crystal structure of right-handed Z-DNA containing 2'-deoxy-L-rib... -

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Basic information

Entry
Database: PDB / ID: 8a71
TitleCrystal structure of right-handed Z-DNA containing 2'-deoxy-L-ribose in complex with the polyamine cadaverine and potassium cations at ultrahigh resolution
ComponentsRight-handed Z-DNA
KeywordsDNA / Z-DNA / Right-handed Z-DNA / Cadaverine / Potassium / Cadaverinium cation / Biogenic polyamines / 2-deoxy-L-ribose
Function / homology: / 5-azaniumylpentylazanium / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.69 Å
AuthorsDrozdzal, P. / Manszewski, T. / Gilski, M. / Brzezinski, K. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2013/10/M/NZ1/00251 Poland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Right-handed Z-DNA at ultrahigh resolution: a tale of two hands and the power of the crystallographic method.
Authors: Drozdzal, P. / Manszewski, T. / Gilski, M. / Brzezinski, K. / Jaskolski, M.
History
DepositionJun 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 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

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Assembly

Deposited unit
A: Right-handed Z-DNA
B: Right-handed Z-DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7644
Polymers3,6202
Non-polymers1432
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-6 kcal/mol
Surface area2500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.914, 31.127, 44.106
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 Right-handed Z-DNA


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Since oligonucleotides contained the enantiomeric 2-deoxy-L-ribose, the Z-DNA duplex is right-handed.
Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-LB9 / 5-azaniumylpentylazanium / cadaverine (protonated)


Mass: 104.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H16N2
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.7 Å3/Da / Density % sol: 27.57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.5 MM DNA WATER SOLUTION MIXED 1:1 V/ V WITH 10% MPD, 14 MM CADAVERINE DI-HCL, 12 MM NACL, 80 MM KCL, 40 MM SODIUM CACODYLATE AND EQUILIBRATED AGAINST 80% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.7085 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7085 Å / Relative weight: 1
ReflectionResolution: 0.69→25.43 Å / Num. obs: 73968 / % possible obs: 96.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 5.963 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.095 / Net I/σ(I): 7.92
Reflection shellResolution: 0.69→0.74 Å / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 10347 / CC1/2: 0.786 / Rrim(I) all: 0.486

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7atg

7atg


Resolution: 0.69→25.43 Å / Cross valid method: FREE R-VALUE
Details: THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. ANISOTROPIC ATOMIC DISPLACEMENT PARAMETERS WERE USED. HYDROGEN ATOMS WERE ADDED AT RIDING POSITION. THE FINAL REFINEMENT WAS ...Details: THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. ANISOTROPIC ATOMIC DISPLACEMENT PARAMETERS WERE USED. HYDROGEN ATOMS WERE ADDED AT RIDING POSITION. THE FINAL REFINEMENT WAS CALCULATED USING WEIGHTED FULL- MATRIX LEAST-SQUARES PROCEDURE AND ALL REFLECTIONS. CONFORMATION-DEPENDENT GEOMETRICAL RESTRAINTS ON BOND LENGTHS AND BOND ANGLES FOR THE POLYNUCLEOTIDE CHAINS WERE GENERATED USING THE RESTRAINLIB SERVER: http://achesym.ibch.poznan.pl/restraintlib/) AS DESCRIBED BY Kowiel et al. (2016, 2020) AND Gilski et al. (2019).
RfactorNum. reflection% reflection
Rfree0.1283 1880 2.54 %
Rwork0.1054 --
obs0.1059 72088 96.3 %
Displacement parametersBiso max: 52.73 Å2 / Biso mean: 7.0004 Å2 / Biso min: 3.09 Å2
Refinement stepCycle: LAST / Resolution: 0.69→25.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 8 121 369

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