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- PDB-8oyr: DNA Major Groove Binding by lambda-[Ru(phen)2(phi)]2+ -

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Basic information

Entry
Database: PDB / ID: 8oyr
TitleDNA Major Groove Binding by lambda-[Ru(phen)2(phi)]2+
ComponentsDNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
KeywordsDNA / Major Groove / B-DNA / Ruthenium complex / ruthenium polypyridyl / decamer / small molecule
Function / homologySTRONTIUM ION / : / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 Å
AuthorsPrieto-Otoya, T.D. / Cardin, C.J. / McQuaid, K.T. / Paterson, N.G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission861381European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Probing a Major DNA Weakness: Resolving the Groove and Sequence Selectivity of the Diimine Complex Lambda-[Ru(phen) 2 phi] 2.
Authors: Prieto Otoya, T.D. / McQuaid, K.T. / Hennessy, J. / Menounou, G. / Gibney, A. / Paterson, N.G. / Cardin, D.J. / Kellett, A. / Cardin, C.J.
History
DepositionMay 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,2186
Polymers3,0461
Non-polymers2,1725
Water1448
1
A: DNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)10,43712
Polymers6,0922
Non-polymers4,34510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
Unit cell
Length a, b, c (Å)56.990, 56.990, 30.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
Components on special symmetry positions
IDModelComponents
11A-101-

V7F

21A-101-

V7F

31A-103-

V7F

41A-203-

HOH

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Components

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


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-V7F / ruthenium polypyridyl complex (lambda enantiomer)


Mass: 665.707 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C38H24N6Ru / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.12 Å3/Da / Density % sol: 70.13 % / Description: red octahedron
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.04 M Strontium Chloride hexahydrate, 0.02 M Sodium cacodylate trihydrate pH 7.0, 10% w/v MPD, 0.006 M spermine tetrahydrochloride, 0.01 M Magnesium chloride hexahydrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763, 0.5585
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
20.55851
ReflectionResolution: 2.21→56.98 Å / Num. obs: 4817 / % possible obs: 100 % / Redundancy: 28.8 % / CC1/2: 0.999 / Net I/σ(I): 21.5
Reflection shellResolution: 2.21→2.25 Å / Rmerge(I) obs: 9.99 / Mean I/σ(I) obs: 0 / Num. unique obs: 132 / CC1/2: 0.094 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata scaling
DIALSdata reduction
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.21→19.66 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 52.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2628 419 10.04 %
Rwork0.2296 --
obs0.2333 2817 85.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 137 8 347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011394
X-RAY DIFFRACTIONf_angle_d1.749632
X-RAY DIFFRACTIONf_dihedral_angle_d32.961120
X-RAY DIFFRACTIONf_chiral_restr0.08139
X-RAY DIFFRACTIONf_plane_restr0.00919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.530.4235860.4445837X-RAY DIFFRACTION57
2.53-3.190.5371640.4311443X-RAY DIFFRACTION100
3.19-19.660.22981690.20031473X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.4673 Å / Origin y: -12.4356 Å / Origin z: 19.1812 Å
111213212223313233
T0.8473 Å20.0528 Å2-0.0384 Å2-0.8365 Å2-0.0072 Å2--0.4924 Å2
L7.293 °24.2552 °2-5.3051 °2-3.8071 °2-3.2262 °2--5.988 °2
S0.4411 Å °-1.637 Å °0.0421 Å °0.2815 Å °-0.6118 Å °0.0785 Å °-0.602 Å °0.8204 Å °0.2476 Å °
Refinement TLS groupSelection details: all

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