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- PDB-8cmm: Re-pairing DNA - binding of a ruthenium phi complex to a double m... -

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Entry
Database: PDB / ID: 8cmm
TitleRe-pairing DNA - binding of a ruthenium phi complex to a double mismatch
ComponentsDNA (5'-D(*CP*GP*CP*TP*AP*TP*AP*AP*TP*GP*CP*G)-3')
KeywordsDNA / DNA mismatch / Ruthenium / Polypyridyl / Intercalation
Function / homology: / : / : / : / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.9 Å
AuthorsPrieto Otoya, T.D. / Cardin, C.J. / McQuaid, K.M.
Funding supportEuropean Union, United Kingdom, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission861381European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008342/1 United Kingdom
CitationJournal: Chem Sci / Year: 2024
Title: Re-pairing DNA: binding of a ruthenium phi complex to a double mismatch.
Authors: Prieto Otoya, T.D. / McQuaid, K.T. / Paterson, N.G. / Cardin, D.J. / Kellett, A. / Cardin, C.J.
History
DepositionFeb 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 2.0Jun 12, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / cell / chem_comp / chem_comp_atom / citation / citation_author / entity / entity_src_gen / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct / struct_asym / struct_conn / symmetry
Item: _cell.volume / _chem_comp.formula ..._cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_R_Free_selection_details / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _software.name / _software.version / _struct.title / _symmetry.space_group_name_Hall
Description: Occupancy of atoms on special symmetry positions
Provider: author / Type: Coordinate replacement
Revision 2.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,0796
Polymers3,6621
Non-polymers1,4175
Water1,26170
1
A: DNA (5'-D(*CP*GP*CP*TP*AP*TP*AP*AP*TP*GP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)10,15812
Polymers7,3252
Non-polymers2,83310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1,-y-1/2,z1
Unit cell
Length a, b, c (Å)31.395, 48.645, 54.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-216-

HOH

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Components

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DNA chain , 1 types, 1 molecules A

#1: DNA chain DNA (5'-D(*CP*GP*CP*TP*AP*TP*AP*AP*TP*GP*CP*G)-3')


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 75 molecules

#2: Chemical ChemComp-V70 / ruthenium polypyridyl complex (delta enantiomer)


Mass: 665.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H24N6Ru / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-V7F / ruthenium polypyridyl complex (lambda enantiomer)


Mass: 665.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H24N6Ru / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Li
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.82 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.01M MgCl2 hexahydrate, 0.05M HEPES sodium, and 4M LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.826 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826 Å / Relative weight: 1
ReflectionResolution: 0.9→36.2 Å / Num. obs: 28800 / % possible obs: 92.5 % / Redundancy: 12.1 % / Biso Wilson estimate: 10.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.013 / Rrim(I) all: 0.046 / Net I/σ(I): 19
Reflection shellResolution: 0.9→0.92 Å / % possible obs: 47.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 2.061 / Num. measured all: 4660 / Num. unique obs: 718 / CC1/2: 0.294 / Rpim(I) all: 0.834 / Rrim(I) all: 2.233 / Net I/σ(I) obs: 0.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
DIALSdata scaling
DIALSdata reduction
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 0.9→36.2 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.667 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1594 1425 4.9 %RANDOM
Rwork0.13592 ---
obs0.137 27375 92.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.224 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0 Å2
2---0.24 Å20 Å2
3---0.29 Å2
Refinement stepCycle: 1 / Resolution: 0.9→36.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 243 93 70 406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013430
X-RAY DIFFRACTIONr_bond_other_d0.0030.018209
X-RAY DIFFRACTIONr_angle_refined_deg2.0782.13679
X-RAY DIFFRACTIONr_angle_other_deg0.6621.863477
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_restr0.1020.255
X-RAY DIFFRACTIONr_gen_planes_refined0.0420.02261
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0298
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_it0.9481.194430
X-RAY DIFFRACTIONr_scbond_other0.9471.193431
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.362.199680
X-RAY DIFFRACTIONr_long_range_B_refined2.14220.03871
X-RAY DIFFRACTIONr_long_range_B_other1.79719.43859
X-RAY DIFFRACTIONr_rigid_bond_restr4.5343639
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.9→0.923 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 60 -
Rwork0.416 1096 -
obs--50.95 %

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