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- PDB-4ymc: Lambda-[Ru(TAP)2(dppz)]2+ bound to d(CCGGATCCGG)2 -

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Basic information

Entry
Database: PDB / ID: 4ymc
TitleLambda-[Ru(TAP)2(dppz)]2+ bound to d(CCGGATCCGG)2
ComponentsDNA (5'-D(*CP*CP*GP*GP*AP*TP*CP*CP*GP*G)-3')
KeywordsDNA / ruthenium / complex / 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
AuthorsGurung, S.P. / Hall, J.P. / Cardin, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K019279/1 United Kingdom
CitationJournal: To Be Published
Title: Reversal of a single base pair step controls guanine photo-oxidation by an intercalating Ru(II) dipyridophenazine complex.
Authors: Keane, P.M. / Gurung, S.P. / Niyazi, H. / Poynton, F.E. / Hall, J.P. / Sazanovich, I.V. / Towrie, M. / Teixeira, S. / Mitchell, E. / Forsyth, T. / Gunnlaugsson, T. / Quinn, S.J. / Cardin, C.J. / Kelly, J.M.
History
DepositionMar 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1May 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
A: DNA (5'-D(*CP*CP*GP*GP*AP*TP*CP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9674
Polymers3,0461
Non-polymers9213
Water36020
1
A: DNA (5'-D(*CP*CP*GP*GP*AP*TP*CP*CP*GP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)7,9338
Polymers6,0922
Non-polymers1,8416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1940 Å2
ΔGint-57 kcal/mol
Surface area4950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.380, 47.380, 33.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-213-

HOH

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Components

#1: DNA chain DNA (5'-D(*CP*CP*GP*GP*AP*TP*CP*CP*GP*G)-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-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.: 20 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The crystals were grown, using the sitting drop method, by adding 1 uL of 2mM d(CCGGATCCGG) and 1 uL 4 mM rac-[Ru(TAP)2(dppz)].2Cl to 6 uL of a solution containing 10% (v/v) 2-methyl-2,4- ...Details: The crystals were grown, using the sitting drop method, by adding 1 uL of 2mM d(CCGGATCCGG) and 1 uL 4 mM rac-[Ru(TAP)2(dppz)].2Cl to 6 uL of a solution containing 10% (v/v) 2-methyl-2,4-pentanediol, 12 mM spermine-tetraHCL, 20mM BaCl2, 80mM KCl and 40 mM Na-cacodylate pH 7. This was equilibrated, at 18 C, against 500 uL 2-methyl-2,4-pentanediol.

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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: Feb 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.88→33.83 Å / Num. obs: 3423 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Rmerge(I) obs: 0.052 / Rsym value: 0.02 / Net I/σ(I): 21.1
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.436 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
Cootmodel building
SHELXphasing
xia2data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.88→33.83 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.915 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25736 149 4.4 %RANDOM
Rwork0.19792 ---
obs0.20028 3250 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.469 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å2-0 Å2
2--0.95 Å20 Å2
3----1.9 Å2
Refinement stepCycle: 1 / Resolution: 1.88→33.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 53 20 275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.013290
X-RAY DIFFRACTIONr_bond_other_d0.030.02134
X-RAY DIFFRACTIONr_angle_refined_deg2.6811.598456
X-RAY DIFFRACTIONr_angle_other_deg4.3723308
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_restr0.110.230
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.02174
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0276
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_it4.3764.667290
X-RAY DIFFRACTIONr_scbond_other4.3084.667289
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1676.982457
X-RAY DIFFRACTIONr_long_range_B_refined5.36148.142630
X-RAY DIFFRACTIONr_long_range_B_other5.37248.141626
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
Rfree0.32 11 -
Rwork0.258 223 -
obs--100 %

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