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- PDB-5iu5: Lambda-[Ru(TAP)2(dppz)]2+ bound to d(TCGGCICCGA)2 -

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Basic information

Entry
Database: PDB / ID: 5iu5
TitleLambda-[Ru(TAP)2(dppz)]2+ bound to d(TCGGCICCGA)2
ComponentsDNA (5'-D(*TP*CP*GP*GP*CP*IP*CP*CP*GP*A)-3')
KeywordsDNA / ruthenium / intercalation / photooxidising
Function / homology: / Ru(tap)2(dppz) complex / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHall, 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: To Be Published
Title: Unexpected enhancement of sensitised photo-oxidation by a Ru(II) complex on replacement of guanine with inosine in DNA
Authors: Keane, P.M. / Hall, J.P. / Poynton, F.E. / Gurung, S.P. / Clark, I.P. / Sazanovich, I.V. / Towrie, M. / Gunnlaugsson, T. / Brazier, J.A. / Quinn, S.J. / Cardin, C.J. / Kelly, J.M.
History
DepositionMar 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,9163
Polymers3,0311
Non-polymers8852
Water21612
1
C: DNA (5'-D(*TP*CP*GP*GP*CP*IP*CP*CP*GP*A)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)7,8326
Polymers6,0622
Non-polymers1,7704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1960 Å2
ΔGint-18 kcal/mol
Surface area4590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.780, 47.780, 33.140
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*IP*CP*CP*GP*A)-3')


Mass: 3030.979 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-RKL / Ru(tap)2(dppz) complex


Mass: 747.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H22N12Ru
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1uL 2mM d(TCGGCICCGA) 1uL 4mM rac-RuTAP2dppz 6uL of a solution containing 20mM BaCl2, 80mM KCl, 40mM Na-cacodylate pH 7, 12mM spermine, 10% (V/V) hexylene glycol

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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: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→47.78 Å / Num. obs: 3067 / % possible obs: 93.9 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.034 / Net I/σ(I): 21.9
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.985 / Mean I/σ(I) obs: 1.6 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→33.786 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 248 4.67 %
Rwork0.1989 --
obs0.1996 3046 91.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→33.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 201 52 12 265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004289
X-RAY DIFFRACTIONf_angle_d2.046454
X-RAY DIFFRACTIONf_dihedral_angle_d24.25697
X-RAY DIFFRACTIONf_chiral_restr0.04238
X-RAY DIFFRACTIONf_plane_restr0.00313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.39370.31831280.28122542X-RAY DIFFRACTION92
2.3937-33.79090.19621200.18592517X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 13.244 Å / Origin y: 11.9997 Å / Origin z: -3.5719 Å
111213212223313233
T0.5296 Å2-0.0147 Å20.0126 Å2-0.3869 Å20.0014 Å2--0.5273 Å2
L8.5056 °2-4.2544 °2-2.6317 °2-4.2024 °23.9555 °2--4.2059 °2
S-0.1817 Å °0.198 Å °-0.2336 Å °-0.1857 Å °-0.1453 Å °0.1468 Å °0.1445 Å °-0.004 Å °0.0215 Å °
Refinement TLS groupSelection details: chain c

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