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- PDB-4qio: Lambda-[Ru(TAP)2(dppz)]2+ bound to d(TCGGCGCCIA) at high resolution -

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Basic information

Entry
Database: PDB / ID: 4qio
TitleLambda-[Ru(TAP)2(dppz)]2+ bound to d(TCGGCGCCIA) at high resolution
Components5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*IP*A)-3'
KeywordsDNA / intercalation / ruthenium complex / inosine
Function / homology: / Ru(tap)2(dppz) complex / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / PDB ENTRY 3QRN / Resolution: 0.95 Å
AuthorsGurung, S.P. / Hall, J.P. / Cardin, C.J.
CitationJournal: Chemistry / Year: 2017
Title: Inosine Can Increase DNA's Susceptibility to Photo-oxidation by a Ru II Complex due to Structural Change in the Minor Groove.
Authors: Keane, P.M. / Hall, J.P. / Poynton, F.E. / Poulsen, B.C. / Gurung, S.P. / Clark, I.P. / Sazanovich, I.V. / Towrie, M. / Gunnlaugsson, T. / Quinn, S.J. / Cardin, C.J. / Kelly, J.M.
History
DepositionJun 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Advisory / Database references
Category: citation / citation_author / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 24, 2022Group: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.0Aug 12, 2026Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / pdbx_entry_details ...chem_comp / pdbx_entry_details / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _chem_comp.formula / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,9514
Polymers3,0311
Non-polymers9213
Water1,44180
1
A: 5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*IP*A)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)7,9038
Polymers6,0622
Non-polymers1,8416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2130 Å2
ΔGint-38 kcal/mol
Surface area4570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.160, 42.160, 39.650
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 5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*IP*A)-3'


Mass: 3030.979 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-RKL / Ru(tap)2(dppz) complex


Mass: 747.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H22N12Ru
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1 uL 1 mM d(TCGGCGCCIA)2 + 1 uL 4 mM rac-Ru(TAP)2(dppz).2Cl + 6uL 40 mM sodium cacodylate, 12 mM spermine, 10% MPD, 20 mM barium chloride, 80 mM potassium chloride equilibrated against 1 mL ...Details: 1 uL 1 mM d(TCGGCGCCIA)2 + 1 uL 4 mM rac-Ru(TAP)2(dppz).2Cl + 6uL 40 mM sodium cacodylate, 12 mM spermine, 10% MPD, 20 mM barium chloride, 80 mM potassium chloride equilibrated against 1 mL 35% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.82565 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82565 Å / Relative weight: 1
ReflectionResolution: 0.95→23.828 Å / Num. all: 22994 / Num. obs: 22994 / % possible obs: 99.5 % / Observed criterion σ(I): -3
Reflection shellResolution: 0.95→0.97 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.8.0071refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: PDB ENTRY 3QRN / Resolution: 0.95→23.828 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.385 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.11928 1179 5.1 %RANDOM
Rwork0.09538 ---
obs0.09655 21791 99.29 %-
all-21791 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.591 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.26 Å2-0 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 0.95→23.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 201 53 80 334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.014337
X-RAY DIFFRACTIONr_bond_other_d0.0020.02156
X-RAY DIFFRACTIONr_angle_refined_deg3.0841.773528
X-RAY DIFFRACTIONr_angle_other_deg1.573360
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_restr0.0960.236
X-RAY DIFFRACTIONr_gen_planes_refined0.0390.02197
X-RAY DIFFRACTIONr_gen_planes_other0.0080.0284
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_it2.5831.355337
X-RAY DIFFRACTIONr_scbond_other2.5791.355338
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5552.011529
X-RAY DIFFRACTIONr_long_range_B_refined4.59914.783750
X-RAY DIFFRACTIONr_long_range_B_other3.83314.136705
X-RAY DIFFRACTIONr_rigid_bond_restr9.0693492
X-RAY DIFFRACTIONr_sphericity_free20.95959
X-RAY DIFFRACTIONr_sphericity_bonded15.0465525
LS refinement shellResolution: 0.95→0.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 84 -
Rwork0.175 1578 -
obs--98.58 %

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