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- PDB-4e8s: Lambda-[Ru(TAP)2(dppz{Me2}2)]2+ bound to TCGGCGCCGA at high resolution -

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Basic information

Entry
Database: PDB / ID: 4e8s
TitleLambda-[Ru(TAP)2(dppz{Me2}2)]2+ bound to TCGGCGCCGA at high resolution
Components5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
KeywordsDNA / Intercalation / Photoreactive / Ruthenium complex
Function / homology: / Chem-RML / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.24 Å
AuthorsHall, J.P. / Cardin, C.J.
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
DepositionMar 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
SupersessionMar 8, 2017ID: 4DX4
Revision 1.2Mar 8, 2017Group: Other
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 28, 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 / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,9954
Polymers3,0461
Non-polymers9493
Water1,820101
1
A: 5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)7,9898
Polymers6,0922
Non-polymers1,8976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area760 Å2
ΔGint-4 kcal/mol
Surface area4260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.400, 42.400, 39.670
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-282-

HOH

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Components

#1: DNA chain 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 / Details: DNA Purchased from ATDBio
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-RML / (11,12-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(2+) / Lambda-[Ru(1,4,5,8-tetraazaphenanthrene)2(11,12-dimethyl-dipyridophenazine)]2+


Mass: 775.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H26N12Ru
#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.: 101 / 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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1ul 2mM DNA, 1ul 2mM Lambda-[Ru(TAP)2(dppz-(Me2))]Cl2, 6ul 10% 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM potassium chloride, 20mM barium chloride, VAPOR ...Details: 1ul 2mM DNA, 1ul 2mM Lambda-[Ru(TAP)2(dppz-(Me2))]Cl2, 6ul 10% 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM potassium chloride, 20mM barium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2012
RadiationMonochromator: Dual Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.24→42.4 Å / Num. all: 10753 / Num. obs: 10743 / % possible obs: 99.9 %
Reflection shellResolution: 1.24→1.27 Å / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
SHELXCDphasing
SHELXEmodel building
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.24→29.98 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.871 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1285 511 4.8 %RANDOM
Rwork0.10321 ---
obs0.10444 10212 99.96 %-
all-10216 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.917 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å2-0 Å2
2--0.45 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.24→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 55 101 358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.013292
X-RAY DIFFRACTIONr_bond_other_d0.0030.02129
X-RAY DIFFRACTIONr_angle_refined_deg2.8451.751460
X-RAY DIFFRACTIONr_angle_other_deg2.443298
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_restr0.120.230
X-RAY DIFFRACTIONr_gen_planes_refined0.0370.02178
X-RAY DIFFRACTIONr_gen_planes_other0.0080.0276
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr9.4623267
X-RAY DIFFRACTIONr_sphericity_free29.0454
X-RAY DIFFRACTIONr_sphericity_bonded18.4695306
LS refinement shellResolution: 1.24→1.272 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 31 -
Rwork0.195 629 -
obs--100 %

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