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- PDB-6r6d: [Ru(TAP)2(11,12-CN2-dppz)]2+ bound to d(TCGGCGCCGA)2 -

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Basic information

Entry
Database: PDB / ID: 6r6d
Title[Ru(TAP)2(11,12-CN2-dppz)]2+ bound to d(TCGGCGCCGA)2
ComponentsDNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')
KeywordsDNA / Ruthenium / intercalation / asymmetric
Function / homology: / Chem-EQQ / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.838 Å
AuthorsMcQuaid, K.T. / Hall, J.P. / Cardin, C.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K019279/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M004635/1 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
DepositionMar 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: 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.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2Nov 11, 2020Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3May 19, 2021Group: Database references / Refinement description
Category: citation / citation_author / pdbx_refine_tls_group
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 / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,0044
Polymers3,0461
Non-polymers9583
Water32418
1
A: DNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)8,0088
Polymers6,0922
Non-polymers1,9166
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2590 Å2
ΔGint-49 kcal/mol
Surface area4340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.704, 46.704, 34.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-EQQ / Ruthenium (bis-(tetraazaphenanthrene)) (11,12-dicyano-dipyridophenazine)


Mass: 797.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H20N14Ru / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.07 Å3/Da / Density % sol: 59.95 % / Description: Orthorhombic
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1uL 1mM dsDNA, 1ul 5mM rac[Ru(TAP)2(11,12-CN2-dppz)]2+, 6ul of a solution containing 10% (v/v) 2-methyl-2,4-pentanediol, 80mM NaCl, 20mM Na-cacodylate pH 7, 20mM BaCl2 and 12mM spermine ...Details: 1uL 1mM dsDNA, 1ul 5mM rac[Ru(TAP)2(11,12-CN2-dppz)]2+, 6ul of a solution containing 10% (v/v) 2-methyl-2,4-pentanediol, 80mM NaCl, 20mM Na-cacodylate pH 7, 20mM BaCl2 and 12mM spermine tetra-HCl equilibrated against 500uL 35% 2-methyl-2,4-pentanediol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.838→34.31 Å / Num. obs: 6316 / % possible obs: 100 % / Redundancy: 23.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.021 / Rrim(I) all: 0.1 / Net I/σ(I): 17.7
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 24.5 % / Num. unique obs: 180 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.15rc2_3433: ???)refinement
xia2data reduction
Aimlessdata scaling
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.838→33.025 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.54
RfactorNum. reflection% reflection
Rfree0.1866 310 4.91 %
Rwork0.1786 --
obs0.179 6316 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.838→33.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 57 18 277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011294
X-RAY DIFFRACTIONf_angle_d1.15462
X-RAY DIFFRACTIONf_dihedral_angle_d26.202101
X-RAY DIFFRACTIONf_chiral_restr0.05442
X-RAY DIFFRACTIONf_plane_restr0.00913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8384-2.31610.30911520.20683013X-RAY DIFFRACTION100
2.3161-33.030.16661580.17292993X-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)
18.8231-5.10142.69688.4054-5.23523.24560.09240.19220.181-0.2833-0.2389-0.12130.20870.07720.22390.3641-0.0370.04790.34270.0230.298133.958935.1409-3.4908
23.0523-2.83931.63717.33963.33685.93530.08050.326-0.08030.3297-0.37840.5280.2641-1.29730.5190.3713-0.0210.00970.4929-0.0170.317646.071530.77711.1266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:10 )A1 - 10
2X-RAY DIFFRACTION2( CHAIN A AND RESID 102:102 )A102

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