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- PDB-8oez: Crystal structure of the Z-DNA hexamer d(CGCGCG) with Iron(II) ch... -

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Basic information

Entry
Database: PDB / ID: 8oez
TitleCrystal structure of the Z-DNA hexamer d(CGCGCG) with Iron(II) chloride
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA
Function / homology: / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsLambert, M.C. / Hall, J.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: To Be Published
Title: Iron binding preferences: observing metal coordination before oxidative damage.
Authors: Lambert, M.C. / Hall, J.P.
History
DepositionMar 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8797
Polymers3,6202
Non-polymers2595
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-40 kcal/mol
Surface area2450 Å2
Unit cell
Length a, b, c (Å)18.094, 30.387, 42.506
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 4 or resid 6))
d_2ens_1(chain "B" and (resid 2 through 4 or resid 6))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-ID
d_11ens_1DGDGA
d_21ens_1DGDGB

NCS oper: (Code: givenMatrix: (0.209394902467, 0.977065595321, 0.0386858793464), (0.976591877247, -0.210957007194, 0.0420172156493), (0.0492146331497, 0.028982124761, -0.998367645874)Vector: -3. ...NCS oper: (Code: given
Matrix: (0.209394902467, 0.977065595321, 0.0386858793464), (0.976591877247, -0.210957007194, 0.0420172156493), (0.0492146331497, 0.028982124761, -0.998367645874)
Vector: -3.83557194011, 4.94528767219, -5.49937158805)

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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: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.61 Å3/Da / Density % sol: 23.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: oligo, 2-methyl-2,4-pentanediol (MPD), sodium cacodylate, pH 6.0, KCl, NaCl and spermine tetrachloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→14.6 Å / Num. obs: 3119 / % possible obs: 99.3 % / Redundancy: 2 % / Biso Wilson estimate: 6.55 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.105 / Net I/σ(I): 13.7
Reflection shellResolution: 1.64→1.7 Å / Rmerge(I) obs: 0.197 / Num. unique obs: 268 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
CrysalisProdata collection
CrysalisProdata scaling
CrysalisProdata reduction
PHENIXphasing
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→14.6 Å / SU ML: 0.1678 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 20.4767
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2243 281 5.16 %
Rwork0.1941 5170 -
obs0.1957 3084 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.65 Å2
Refinement stepCycle: LAST / Resolution: 1.64→14.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 5 52 297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0165308
X-RAY DIFFRACTIONf_angle_d1.6861474
X-RAY DIFFRACTIONf_chiral_restr0.13353
X-RAY DIFFRACTIONf_plane_restr0.010314
X-RAY DIFFRACTIONf_dihedral_angle_d30.9185134
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.414038578808 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-2.070.25041420.2392557X-RAY DIFFRACTION98.25
2.07-14.60.20891390.17012613X-RAY DIFFRACTION99.71

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