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- PDB-8rer: Major groove intercalation with Polypyridyl Ruthenium complex -

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Basic information

Entry
Database: PDB / ID: 8rer
TitleMajor groove intercalation with Polypyridyl Ruthenium complex
Components
  • DNA (5'-D(*CP*CP*TP*AP*TP*TP*C)-3')
  • DNA (5'-D(*GP*AP*AP*TP*AP*GP*G)-3')
KeywordsDNA / Major Groove / ruthenium / Minor Groove
Function / homologylambda-[Ru(tap2-dppz-CN)]2+ / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsAbdullrahman, A. / Cardin, C.J. / Hall, J.P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionH2020-MSCA-INT-2019-861European Union
CitationJournal: To Be Published
Title: Ruthenium Polypyridyl complex intercalating in Major and Minor Groove DNA
Authors: Abdullrahman, A. / McQuaid, K. / Cardin, C.J. / Hall, J.P.
History
DepositionDec 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,96822
Polymers8,4704
Non-polymers3,49818
Water3,729207
1
A: DNA (5'-D(*GP*AP*AP*TP*AP*GP*G)-3')
B: DNA (5'-D(*CP*CP*TP*AP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,01912
Polymers4,2352
Non-polymers1,78510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*GP*AP*AP*TP*AP*GP*G)-3')
D: DNA (5'-D(*CP*CP*TP*AP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,94810
Polymers4,2352
Non-polymers1,7148
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.676, 32.676, 103.988
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "C"
d_1ens_2chain "B"
d_2ens_2chain "D"

NCS domain segments:

Component-ID: 1 / Auth seq-ID: 1 / Label seq-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-ID
d_1ens_1DGDGDGDGAA
d_2ens_1DGDGDGDGCC
d_1ens_2DCDCDCDCBB
d_2ens_2DCDCDCDCDD

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999998178393, -0.000623046296423, 0.00180416823599), (-0.000624976034436, 0.999999233072, -0.00106923364807), (-0.00180350067025, -0.00107035926226, -0.999997800856)16.3388986035, -16.3278197104, 26.1927609427
2given(-0.99999907835, -0.000941983179922, 0.000977736000587), (-0.000942032803414, 0.999999555022, -5.02941783372E-5), (-0.000977688189246, -5.12151913692E-5, -0.999999520751)16.324011143, -16.3268421834, 26.1884389207

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Components

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DNA chain , 2 types, 4 molecules ACBD

#1: DNA chain DNA (5'-D(*GP*AP*AP*TP*AP*GP*G)-3')


Mass: 2186.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*CP*TP*AP*TP*TP*C)-3')


Mass: 2048.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 225 molecules

#3: Chemical
ChemComp-KSB / lambda-[Ru(tap2-dppz-CN)]2+ / Cyano-derivative of Ruthenium-dipyridophenazine


Type: D-beta-peptide, C-gamma linking / Mass: 772.741 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H21N13Ru / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.28 Å3/Da / Density % sol: 62.47 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.86
Details: A solution containing 0.6 mM DNA, 20 mM Sodium Cacodylate pH 5.5, 100 mM NaCl, 10 mM MgCl2 and 1.6 mM [Ru(TAP)2(11-CN-dppz)] was mixed in a 1:1 ratio with a solution containing 80.6 mM KCl, ...Details: A solution containing 0.6 mM DNA, 20 mM Sodium Cacodylate pH 5.5, 100 mM NaCl, 10 mM MgCl2 and 1.6 mM [Ru(TAP)2(11-CN-dppz)] was mixed in a 1:1 ratio with a solution containing 80.6 mM KCl, 40 mM Sodium cacodylate trihydrate pH 5.86, 55% -2-Methyl-2,4-pentanediol, 120 mM Spermine tetrahydrochloride.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.2→32.68 Å / Num. obs: 33977 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 15.77 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.02 / Rrim(I) all: 0.072 / Net I/σ(I): 0.828
Reflection shellResolution: 1.2→3.26 Å / Num. unique obs: 1710 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
xia2data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→32.68 Å / SU ML: 0.2273 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.9477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2025 3234 5.08 %
Rwork0.1715 60407 -
obs0.173 32448 94.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.31 Å2
Refinement stepCycle: LAST / Resolution: 1.2→32.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 562 226 207 995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062958
X-RAY DIFFRACTIONf_angle_d2.26731522
X-RAY DIFFRACTIONf_chiral_restr0.0426108
X-RAY DIFFRACTIONf_plane_restr0.003543
X-RAY DIFFRACTIONf_dihedral_angle_d30.1066294
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.089533346448
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.0274694903101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.4673130.6545490X-RAY DIFFRACTION17
1.22-1.240.56961890.56572434X-RAY DIFFRACTION91.59
1.24-1.260.53791450.53532496X-RAY DIFFRACTION88.89
1.26-1.280.55391200.50722708X-RAY DIFFRACTION99.23
1.28-1.30.48291800.48292731X-RAY DIFFRACTION99.18
1.3-1.330.51581160.44972786X-RAY DIFFRACTION99.42
1.33-1.350.46131360.40872819X-RAY DIFFRACTION99.7
1.35-1.380.41851520.37362708X-RAY DIFFRACTION99.24
1.38-1.420.3277930.3072857X-RAY DIFFRACTION99.26
1.42-1.450.33171580.26912710X-RAY DIFFRACTION99.45
1.45-1.490.2441650.2532832X-RAY DIFFRACTION99.67
1.49-1.530.22171580.21782654X-RAY DIFFRACTION98.81
1.53-1.580.20781760.20172711X-RAY DIFFRACTION98.67
1.58-1.640.19921680.17832703X-RAY DIFFRACTION97.69
1.64-1.710.15361020.15062748X-RAY DIFFRACTION97.17
1.71-1.780.17841850.15492681X-RAY DIFFRACTION98.15
1.78-1.880.15521430.14912725X-RAY DIFFRACTION99.07
1.88-20.20571330.15482761X-RAY DIFFRACTION99.59
2-2.150.14191200.13572830X-RAY DIFFRACTION99.33
2.15-2.370.13951340.13922767X-RAY DIFFRACTION99.52
2.37-2.710.15781560.13832779X-RAY DIFFRACTION99.97
2.71-3.410.18321550.13622694X-RAY DIFFRACTION98.55
3.41-32.680.15121370.10522783X-RAY DIFFRACTION99.49

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