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- PDB-3qrn: X-ray crystal structure of the ruthenium complex [Ru(tap)2(dppz)]... -

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Basic information

Entry
Database: PDB / ID: 3qrn
TitleX-ray crystal structure of the ruthenium complex [Ru(tap)2(dppz)]2+ bound to d(TCGGCGCCGA)at high resolution
Components5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
KeywordsDNA / intercalation / semi-intercalation / B-DNA
Function / homology: / Ru(tap)2(dppz) complex / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsCardin, C.J. / Hall, J.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand.
Authors: Hall, J.P. / O'Sullivan, K. / Naseer, A. / Smith, J.A. / Kelly, J.M. / Cardin, C.J.
History
DepositionFeb 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9313
Polymers3,0461
Non-polymers8852
Water1,15364
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)7,8626
Polymers6,0922
Non-polymers1,7704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area760 Å2
ΔGint-4 kcal/mol
Surface area4250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.320, 42.320, 39.870
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(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-RKL / Ru(tap)2(dppz) complex


Mass: 747.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H22N12Ru
#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.: 64 / 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: 58.03 %
Crystal growTemperature: 276 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10%(v/v) 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM sodium chloride, 20mM barium chloride, 1mM DNA d(TCGGCGCCGA), 1mM lambda-[Ru(tap)2dppz)Cl2, pH 7, ...Details: 10%(v/v) 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM sodium chloride, 20mM barium chloride, 1mM DNA d(TCGGCGCCGA), 1mM lambda-[Ru(tap)2dppz)Cl2, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 276K

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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: Feb 16, 2011
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.1→21.16 Å / Num. all: 15135 / Num. obs: 14312 / % possible obs: 88.14 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.066
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 16 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 6.1 / Num. unique all: 2160 / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QF8

3qf8


Resolution: 1.1→18.93 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.12445 761 5 %RANDOM
Rwork0.10671 ---
obs0.10755 13340 99.37 %-
all-14402 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.1→18.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 52 64 318
LS refinement shellResolution: 1.102→1.131 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 61 -
Rwork0.275 1031 -
obs--100 %

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