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- PDB-5iwj: LAmbda-[Ru(TAP)2(dppz)]2+ bound to d(CCGGGCCCGG -

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Basic information

Entry
Database: PDB / ID: 5iwj
TitleLAmbda-[Ru(TAP)2(dppz)]2+ bound to d(CCGGGCCCGG
ComponentsDNA (5'-D(*CP*CP*GP*GP*GP*CP*CP*CP*GP*G)-3')
KeywordsDNA / Ruthenium / photooxidising / intercalation
Function / homology: / Ru(tap)2(dppz) complex / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsSouter, J.E. / 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: To Be Published
Title: The binding specificity of RuTAP2dppz
Authors: Souter, J.E. / Hall, J.P. / Gurung, S.P. / Brazier, J.A. / Cardin, C.J.
History
DepositionMar 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,9323
Polymers3,0471
Non-polymers8852
Water54030
1
C: DNA (5'-D(*CP*CP*GP*GP*GP*CP*CP*CP*GP*G)-3')
hetero molecules

C: DNA (5'-D(*CP*CP*GP*GP*GP*CP*CP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8646
Polymers6,0942
Non-polymers1,7704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_774-y+2,-x+2,-z-1/21
Buried area2050 Å2
ΔGint-25 kcal/mol
Surface area4380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.783, 46.783, 34.948
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(*CP*CP*GP*GP*GP*CP*CP*CP*GP*G)-3')


Mass: 3046.980 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.: 30 / 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: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1uL 2mM ss oligonucleotide, 1uL 3mM rac-RuTAP2dppz, 6uL of a solution containing 20mM BaCl2, 80mM KCl, 10% (V/V) hexylene glycol, 12mM spermine, 40mM Na-cacodylate pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.88→28 Å / Num. obs: 3455 / % possible obs: 100 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.2
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.939 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
xia2data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.88→28 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.736 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.159 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27716 193 5.7 %RANDOM
Rwork0.21048 ---
obs0.21403 3207 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.684 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.82 Å20 Å2
3---1.63 Å2
Refinement stepCycle: 1 / Resolution: 1.88→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 52 30 284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013290
X-RAY DIFFRACTIONr_bond_other_d0.0020.02133
X-RAY DIFFRACTIONr_angle_refined_deg2.3231.592456
X-RAY DIFFRACTIONr_angle_other_deg1.4633305
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_restr0.0660.230
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02176
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0280
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_it2.2535.12290
X-RAY DIFFRACTIONr_scbond_other2.2495.12289
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1927.64457
X-RAY DIFFRACTIONr_long_range_B_refined5.17153.441215
X-RAY DIFFRACTIONr_long_range_B_other5.11253.4331201
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 11 -
Rwork0.333 217 -
obs--96.2 %

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