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- PDB-6g8s: [Ru(TAP)2(11,12-CN2-dppz)]2+ bound to d(CCGGACCCGG/CCGGGTCCGG)2 -

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Basic information

Entry
Database: PDB / ID: 6g8s
Title[Ru(TAP)2(11,12-CN2-dppz)]2+ bound to d(CCGGACCCGG/CCGGGTCCGG)2
Components
  • DNA (5'-D(*CP*CP*GP*GP*AP*CP*CP*CP*GP*G)-3')
  • DNA (5'-D(*CP*CP*GP*GP*GP*TP*CP*CP*GP*G)-3')
KeywordsDNA / Ruthenium / intercalation / asymmetric
Function / homology: / Chem-EQQ / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.66 Å
AuthorsMcQuaid, K.T. / Hall, J.P. / Cardin, C.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K019279/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M004635/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P021328/1 United Kingdom
CitationJournal: Chemistry / Year: 2018
Title: X-ray Crystal Structures Show DNA Stacking Advantage of Terminal Nitrile Substitution in Ru-dppz Complexes.
Authors: McQuaid, K. / Hall, J.P. / Brazier, J.A. / Cardin, D.J. / Cardin, C.J.
History
DepositionApr 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,9636
Polymers6,0932
Non-polymers1,8704
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-32 kcal/mol
Surface area4480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.247, 47.247, 33.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

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


Mass: 3061.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*CP*GP*GP*AP*CP*CP*CP*GP*G)-3')


Mass: 3030.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#4: Chemical ChemComp-EQQ / Ruthenium (bis-(tetraazaphenanthrene)) (11,12-dicyano-dipyridophenazine)


Mass: 797.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H20N14Ru
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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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: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystallisation was observed in a number of conditions from the Nucleic Acid Mini-Screen from Hampton Research, where the best diffracting example came from a 8uL drop containing; 125 uM ...Details: Crystallisation was observed in a number of conditions from the Nucleic Acid Mini-Screen from Hampton Research, where the best diffracting example came from a 8uL drop containing; 125 uM d(CCGGACCCGG/CCGGGTCCGG)2, 750 uM rac-[Ru(TAP)2(11,12-CN2-dppz)]2+, 7.5% v/v MPD, 30 mM pH 7 sodium cacodylate, 9 mM spermine tetrahydrochloride, 60 mM KCl and 15 mM BaCl2; all equilibrated against 1 mL of 35% v/v MPD. Orange/red rods grew following roughly 3 weeks of incubation at 291 K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 23, 2017
RadiationMonochromator: Dual Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.66→27.59 Å / Num. obs: 9018 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.015 / Rrim(I) all: 0.053 / Net I/σ(I): 23.9
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 13 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 460 / CC1/2: 0.652 / Rpim(I) all: 0.261 / Rrim(I) all: 0.942 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DIALSdata reduction
Aimlessdata scaling
SHELXCDphasing
xia2data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.66→23.623 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 31.09
RfactorNum. reflection% reflection
Rfree0.2034 941 5.42 %
Rwork0.1873 --
obs0.1883 9018 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.66→23.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 112 68 584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005638
X-RAY DIFFRACTIONf_angle_d0.9391002
X-RAY DIFFRACTIONf_dihedral_angle_d27.173222
X-RAY DIFFRACTIONf_chiral_restr0.04592
X-RAY DIFFRACTIONf_plane_restr0.00428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6601-1.74760.39341300.39622356X-RAY DIFFRACTION100
1.7476-1.8570.43281180.33892352X-RAY DIFFRACTION100
1.857-2.00030.27221380.29092366X-RAY DIFFRACTION100
2.0003-2.20150.18661280.23072323X-RAY DIFFRACTION100
2.2015-2.51980.26341270.19892374X-RAY DIFFRACTION100
2.5198-3.17340.24381350.19982337X-RAY DIFFRACTION100
3.1734-23.62580.16391650.14832312X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.92370.70910.16050.53150.11150.07680.5678-0.2128-0.12780.3363-0.3987-0.09980.4403-0.2690.01630.45260.0729-0.03510.4765-0.05390.396514.254513.19735.5714
20.27260.4732-0.19350.7806-0.32040.1399-0.23320.217-0.15150.08450.3835-0.0782-0.15790.37840.00020.42140.0946-0.06120.4491-0.05610.371811.779110.849-3.4934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 10 )

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