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- PDB-4x1a: Lambda-[Ru(TAP)2(dppz-10,12-Me)]2+ bound to d(TCGGCGCCGA) -

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Basic information

Entry
Database: PDB / ID: 4x1a
TitleLambda-[Ru(TAP)2(dppz-10,12-Me)]2+ bound to d(TCGGCGCCGA)
ComponentsDNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')
KeywordsDNA / Ruthenium / polypyridyl
Function / homologyChem-3WB / : / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.89 Å
AuthorsHall, J.P. / Cardin, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K019279/1 United Kingdom
CitationJournal: Organometallics / Year: 2015
Title: The Structural Effect of Methyl Substitution on the Binding of Polypyridyl Ru-dppz Complexes to DNA
Authors: Hall, J.P. / Beer, H. / Buchner, K. / Cardin, D.J. / Cardin, C.J.
History
DepositionNov 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / 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.auth_seq_id / _atom_site.label_alt_id / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _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_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,9593
Polymers3,0461
Non-polymers9132
Water1,63991
1
A: DNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)7,9186
Polymers6,0922
Non-polymers1,8264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area1680 Å2
ΔGint-21 kcal/mol
Surface area4590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.250, 42.250, 39.550
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-273-

HOH

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Components

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


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-3WB / (10,12-dimethyldipyrido[3,2-a:2',3'-c]phenazine-kappa~2~N~4~,N~5~)[bis(pyrazino[2,3-f]quinoxaline-kappa~2~N~1~,N~10~)]ruthenium


Mass: 775.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H26N12Ru
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1uL 2mM d(TCGGCGCCGA), 1ul 4mM rac-[Ru(TAP)2(dppz-10,12-Me)]2+, 6ul of a solution containing 20mM BaCl2, 80mM KCl, 12mM Spermine, 40mM Na-cacodylate pH 7, 10% v/v 2-methyl-2,4-pentanediol. ...Details: 1uL 2mM d(TCGGCGCCGA), 1ul 4mM rac-[Ru(TAP)2(dppz-10,12-Me)]2+, 6ul of a solution containing 20mM BaCl2, 80mM KCl, 12mM Spermine, 40mM Na-cacodylate pH 7, 10% v/v 2-methyl-2,4-pentanediol. Equilibrated against 1ml 35% v/v 2-methyl-2,4-pentanediol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 0.89→17.05 Å / Num. obs: 27563 / % possible obs: 98.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 23.5
Reflection shellResolution: 0.89→0.91 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2.2 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 0.89→17.05 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.989 / SU B: 0.268 / SU ML: 0.007 / Cross valid method: THROUGHOUT / ESU R: 0.011 / ESU R Free: 0.011 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.10627 1372 5 %RANDOM
Rwork0.09569 ---
obs0.09623 26155 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.688 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å2-0 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 0.89→17.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 54 91 347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.040.013292
X-RAY DIFFRACTIONr_bond_other_d0.0020.02138
X-RAY DIFFRACTIONr_angle_refined_deg2.7561.61460
X-RAY DIFFRACTIONr_angle_other_deg1.4653316
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_restr0.0730.230
X-RAY DIFFRACTIONr_gen_planes_refined0.040.02178
X-RAY DIFFRACTIONr_gen_planes_other0.0090.0276
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_it1.8141.159292
X-RAY DIFFRACTIONr_scbond_other1.812293
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1261.737461
X-RAY DIFFRACTIONr_long_range_B_refined3.57914.328746
X-RAY DIFFRACTIONr_long_range_B_other2.358695
X-RAY DIFFRACTIONr_rigid_bond_restr7.4273292
X-RAY DIFFRACTIONr_sphericity_free37.855517
X-RAY DIFFRACTIONr_sphericity_bonded10.6835331
LS refinement shellResolution: 0.89→0.913 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 116 -
Rwork0.215 1809 -
obs--95.34 %

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