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- PDB-8pip: DNA triplex structure with Polypyridyl Ruthenium Complexes -

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Basic information

Entry
Database: PDB / ID: 8pip
TitleDNA triplex structure with Polypyridyl Ruthenium Complexes
ComponentsDNA (31-MER)
KeywordsDNA / triplex / triple helix / ruthenium
Function / homologyDelta-Ru(phen)2(dppz) complex / Lambda-Ru(phen)2(dppz) complex / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsAbdullrahman, A. / Cardin, C.J. / Hall, J.P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionH2020-MSCA-ITN-2019-861381European Union
CitationJournal: To Be Published
Title: DNA triplex structure with bound ruthenium polypyridyl complexes
Authors: Abdullrahman, A. / McQuaid, K. / Cardin, C.J. / Hall, J.P.
History
DepositionJun 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (31-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6896
Polymers9,3871
Non-polymers2,3025
Water1,45981
1
A: DNA (31-MER)
hetero molecules

A: DNA (31-MER)
hetero molecules

A: DNA (31-MER)
hetero molecules

A: DNA (31-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,75724
Polymers37,5484
Non-polymers9,20920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area10000 Å2
ΔGint-126 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.464, 86.151, 87.852
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: DNA chain DNA (31-MER)


Mass: 9387.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-0TN / Delta-Ru(phen)2(dppz) complex


Mass: 743.779 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H26N8Ru
#3: Chemical ChemComp-RKP / Lambda-Ru(phen)2(dppz) complex


Mass: 743.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H26N8Ru
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.78 Å3/Da / Density % sol: 67.42 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.16
Details: A solution containing 20mM Na-cacodylate, 10mM MgCl2, 1.6mM DNA, 1.6mM rac-[Ru(phen)2(dppz)].2Cl was mixed in a 1:1 ratio with a solution containing 1.8mM LiSO4, 50mM tris-HCL pH 7.16, 1.4mM ...Details: A solution containing 20mM Na-cacodylate, 10mM MgCl2, 1.6mM DNA, 1.6mM rac-[Ru(phen)2(dppz)].2Cl was mixed in a 1:1 ratio with a solution containing 1.8mM LiSO4, 50mM tris-HCL pH 7.16, 1.4mM CuCl2 and 0.6mM spermine. Total drop volume was 400nL

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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: Feb 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20.34 Å / Num. obs: 9970 / % possible obs: 99.9 % / Redundancy: 40.3 % / Biso Wilson estimate: 32.33 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.043 / Net I/σ(I): 15.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 3.62 / Num. unique obs: 717 / CC1/2: 0.84 / Rpim(I) all: 0.94

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→20.34 Å / SU ML: 0.1059 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.0571
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2585 925 5.05 %
Rwork0.2293 17409 -
obs0.2309 9886 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.05 Å2
Refinement stepCycle: LAST / Resolution: 2→20.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 621 155 81 857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045928
X-RAY DIFFRACTIONf_angle_d1.81421461
X-RAY DIFFRACTIONf_chiral_restr0.0406131
X-RAY DIFFRACTIONf_plane_restr0.002742
X-RAY DIFFRACTIONf_dihedral_angle_d32.2544344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.36061370.37282434X-RAY DIFFRACTION97.57
2.11-2.240.36391230.32272526X-RAY DIFFRACTION99.21
2.24-2.410.34551050.36592423X-RAY DIFFRACTION95.79
2.41-2.650.29461450.31092507X-RAY DIFFRACTION99.66
2.65-3.030.42721320.27932505X-RAY DIFFRACTION99.47
3.03-3.820.19091370.19142509X-RAY DIFFRACTION99.66
3.82-20.340.2041460.15352505X-RAY DIFFRACTION99.81
Refinement TLS params.Method: refined / Origin x: 33.4523698087 Å / Origin y: 31.1468162734 Å / Origin z: -4.79920120896 Å
111213212223313233
T0.18521361015 Å2-0.0267132290976 Å2-0.0981576418876 Å2-0.245450584741 Å2-0.0192858642668 Å2--0.216412699498 Å2
L1.18296308488 °20.190996980422 °2-0.191861041446 °2-2.04659432972 °20.0830618364731 °2--2.08186513228 °2
S0.321004531127 Å °0.114727175191 Å °-0.0842744955235 Å °0.00166441081256 Å °-0.0984872446332 Å °-0.0825889273953 Å °0.402565236613 Å °-0.310666950553 Å °-0.112632209537 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 31)

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