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- PDB-5nbe: [Ru(TAP)2(dppz-11-CN)]2+ bound to d(TCGGCGCCGA)2 -

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Basic information

Entry
Database: PDB / ID: 5nbe
Title[Ru(TAP)2(dppz-11-CN)]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: / lambda-[Ru(tap2-dppz-CN)]2+ / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.51 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 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: 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 2.0Dec 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.id / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Jan 10, 2024Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)3,9563
Polymers3,0461
Non-polymers9102
Water1,17165
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)7,9126
Polymers6,0922
Non-polymers1,8204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2080 Å2
ΔGint-20 kcal/mol
Surface area4510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.880, 47.880, 29.140
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-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.: 1 / Source method: obtained synthetically / Formula: C39H21N13Ru
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1uL 1mM dsDNA, 1ul 4mM rac[Ru(TAP)2(dppz-11-CM)]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- ...Details: 1uL 1mM dsDNA, 1ul 4mM rac[Ru(TAP)2(dppz-11-CM)]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
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 20, 2016
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: 1.51→24.89 Å / Num. obs: 5452 / % possible obs: 96.7 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.039 / Net I/σ(I): 11.4
Reflection shellResolution: 1.51→1.55 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.318 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 394 / CC1/2: 0.593 / Rpim(I) all: 0.588 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
xia2data reduction
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.51→24.89 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.024 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19033 281 5.2 %RANDOM
Rwork0.16482 ---
obs0.16628 5156 95.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.271 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å2-0 Å2-0 Å2
2--0.73 Å2-0 Å2
3----1.47 Å2
Refinement stepCycle: 1 / Resolution: 1.51→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 54 65 321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.014358
X-RAY DIFFRACTIONr_bond_other_d0.0030.02154
X-RAY DIFFRACTIONr_angle_refined_deg2.8691.88571
X-RAY DIFFRACTIONr_angle_other_deg1.463348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0520.230
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02231
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0298
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2112.178358
X-RAY DIFFRACTIONr_scbond_other1.2092.177359
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.833.249572
X-RAY DIFFRACTIONr_long_range_B_refined3.10217.027987
X-RAY DIFFRACTIONr_long_range_B_other3.117.025988
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 20 -
Rwork0.312 373 -
obs--96.8 %

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