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- PDB-4e95: Lambda-[Ru(TAP)2(dppz-(Me)2)]2+ bound to CCGGATCCGG -

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Basic information

Entry
Database: PDB / ID: 4.0E+95
TitleLambda-[Ru(TAP)2(dppz-(Me)2)]2+ bound to CCGGATCCGG
Components5'-D(*CP*CP*GP*GP*AP*TP*CP*CP*GP*G)-3'
KeywordsDNA / Intercalation / Photoreactive / Lambda-[Ru(TAP)2(dppz-(Me)2]2+
Function / homology: / Chem-RML / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 Å
AuthorsHall, J.P. / Cardin, C.J.
CitationJournal: Thesis, University of Reading / Year: 2014
Title: The effects of disubstitution on the binding of ruthenium complexes to DNA
Authors: Hall, J.P.
History
DepositionMar 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,9593
Polymers3,0461
Non-polymers9132
Water68538
1
A: 5'-D(*CP*CP*GP*GP*AP*TP*CP*CP*GP*G)-3'
hetero molecules

A: 5'-D(*CP*CP*GP*GP*AP*TP*CP*CP*GP*G)-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 operation7_553y,x,-z-21
Buried area2120 Å2
ΔGint-24 kcal/mol
Surface area4410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.440, 47.440, 34.530
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 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 / Details: DNA Purchased from ATDBio / 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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1ul 2mM DNA, 1ul 4mM lambda-[Ru(TAP)2(dppz-(Me)2]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 4mM lambda-[Ru(TAP)2(dppz-(Me)2]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 298K

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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 12, 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: 1.94→34.53 Å / Num. all: 3219 / Num. obs: 3216 / % possible obs: 99.9 %
Reflection shellResolution: 1.94→1.99 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: 1.94→33.55 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.908 / SU B: 2.865 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.15
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24635 139 4.4 %RANDOM
Rwork0.18331 ---
obs0.18603 3055 100 %-
all-3055 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.236 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.94→33.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 54 38 294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.013292
X-RAY DIFFRACTIONr_bond_other_d0.0020.02129
X-RAY DIFFRACTIONr_angle_refined_deg3.7071.751460
X-RAY DIFFRACTIONr_angle_other_deg1.7123298
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_restr0.0880.230
X-RAY DIFFRACTIONr_gen_planes_refined0.0290.02176
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0274
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 4 -
Rwork0.281 190 -
obs--100 %

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