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- PDB-6hwg: [Ru(phen)2(dppz-11-CN)]2+ bound to d(TCGGCGCCGA)2 -

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Basic information

Entry
Database: PDB / ID: 6hwg
Title[Ru(phen)2(dppz-11-CN)]2+ bound to d(TCGGCGCCGA)2
ComponentsDNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')
KeywordsDNA / Ruthenium / intercalation / asymmetric
Function / homology: / Chem-GWQ / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.74 Å
AuthorsMcQuaid, K.T. / Hall, J.P. / Cardin, C.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K019279/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M004635/1 United Kingdom
CitationJournal: To Be Published
Title: [Ru(phen)2(dppz-11-CN)]2+ bound to d(TCGGCGCCGA)2
Authors: McQuaid, K.T. / Hall, J.P. / Cardin, C.J.
History
DepositionOct 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 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_asym_id / _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_asym_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_asym_id / _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_asym_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

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


Theoretical massNumber of molelcules
Total (without water)7,9046
Polymers6,0922
Non-polymers1,8124
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-26 kcal/mol
Surface area4520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.936, 47.936, 33.632
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-GWQ / Ruthenium (bis-(phenanthroline)) (11-cyano-dipyridophenazine)


Mass: 768.789 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C43H25N9Ru
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.17 Å3/Da / Density % sol: 61.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1uL 1mM dsDNA, 1ul 3mM L-[Ru(phen)2(dppz-11-CN)]2+, 6ul of a solution containing 10% (v/v) 2-methyl-2,4-pentanediol, 80mM NaCl, 20mM Na-cacodylate pH 7, 20mM BaCl2 and 12mM spermine tetra- ...Details: 1uL 1mM dsDNA, 1ul 3mM L-[Ru(phen)2(dppz-11-CN)]2+, 6ul of a solution containing 10% (v/v) 2-methyl-2,4-pentanediol, 80mM NaCl, 20mM Na-cacodylate pH 7, 20mM BaCl2 and 12mM spermine tetra-HCl equilibrated against 500uL 35% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2017
RadiationMonochromator: dual Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.74→33.9 Å / Num. obs: 7989 / % possible obs: 99.94 % / Redundancy: 2 % / Biso Wilson estimate: 28.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03763 / Rpim(I) all: 0.03763 / Rrim(I) all: 0.05322 / Net I/σ(I): 11.05
Reflection shellResolution: 1.74→1.803 Å / Redundancy: 2 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 1.76 / Num. unique obs: 805 / CC1/2: 0.382 / Rpim(I) all: 0.358 / Rrim(I) all: 0.5063 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
XDSdata reduction
pointlessdata scaling
Cootmodel building
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.74→33.896 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 24.1
RfactorNum. reflection% reflection
Rfree0.2055 799 5.21 %
Rwork0.1939 --
obs0.1946 7989 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.59 Å2
Refinement stepCycle: LAST / Resolution: 1.74→33.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 108 83 595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011650
X-RAY DIFFRACTIONf_angle_d1.3851030
X-RAY DIFFRACTIONf_dihedral_angle_d26.501207
X-RAY DIFFRACTIONf_chiral_restr0.06587
X-RAY DIFFRACTIONf_plane_restr0.01229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7405-1.84950.33031330.33982441X-RAY DIFFRACTION100
1.8495-1.99230.30991340.30772444X-RAY DIFFRACTION99
1.9923-2.19280.29081630.24652348X-RAY DIFFRACTION100
2.1928-2.510.25691180.20492440X-RAY DIFFRACTION100
2.51-3.1620.25981270.19682428X-RAY DIFFRACTION100
3.162-33.90210.13141240.15052438X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.5622-3.08293.46955.8336-2.29012.0653-0.0288-0.0461-0.14850.57080.14250.2434-0.3797-0.2368-0.05760.3311-0.09780.04270.3623-0.03810.307512.5943-12.41745.0311
25.9534-3.80422.77394.8633-3.82282.99950.13660.4401-0.2694-0.0932-0.00060.25010.12730.3315-0.16610.3824-0.08870.0210.2883-0.0490.315711.6029-11.3734-1.9733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 10 )

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