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- PDB-5lfx: Lambda-[Ru(phen)2(dppz-11,12-Me)]2+ bound to a short substituted ... -

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Basic information

Entry
Database: PDB / ID: 5lfx
TitleLambda-[Ru(phen)2(dppz-11,12-Me)]2+ bound to a short substituted DNA sequence
Components
  • DNA (5'-D(*(CBR)P*GP*GP*C)-3')
  • DNA (5'-D(*GP*CP*CP*G)-3')
KeywordsDNA / Ruthenium / light-switch / intercalation
Function / homologyRu(phen)2(dppz-11,12-Me2) / : / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.56 Å
AuthorsHall, 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/M006435/1 United Kingdom
CitationJournal: Chemistry / Year: 2017
Title: Guanine Can Direct Binding Specificity of Ru-dipyridophenazine (dppz) Complexes to DNA through Steric Effects.
Authors: Hall, J.P. / Gurung, S.P. / Henle, J. / Poidl, P. / Andersson, J. / Lincoln, P. / Winter, G. / Sorensen, T. / Cardin, D.J. / Brazier, J.A. / Cardin, C.J.
History
DepositionJul 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*CP*G)-3')
C: DNA (5'-D(*(CBR)P*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,2924
Polymers2,3832
Non-polymers9092
Water88349
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-10 kcal/mol
Surface area2050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.720, 67.720, 35.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11C-111-

HOH

21C-121-

HOH

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Components

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


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*(CBR)P*GP*GP*C)-3')


Mass: 1190.734 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#4: Chemical ChemComp-9ZQ / Ru(phen)2(dppz-11,12-Me2)


Mass: 771.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H30N8Ru
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 4.98 Å3/Da / Density % sol: 75.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1ul 2mM DNA (single stranded), 1uL 4mM rac-[Ru(phen)2(dppz-11,12-Me)]2+, 6uL of 10% 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine, 80mM KCl, 20mM BaCl2. Equilibrated ...Details: 1ul 2mM DNA (single stranded), 1uL 4mM rac-[Ru(phen)2(dppz-11,12-Me)]2+, 6uL of 10% 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine, 80mM KCl, 20mM BaCl2. Equilibrated against 1ml 2-methyl-2,4-pentanediol, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.8266 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.56→35.85 Å / Num. obs: 7169 / % possible obs: 98.2 % / Observed criterion σ(F): -3 / Redundancy: 9.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.8
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.984 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.883 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
xia2data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.56→35.85 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.974 / SU B: 4.191 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.06 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 367 5.1 %RANDOM
Rwork0.14386 ---
obs0.14621 6787 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.488 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å2-0.65 Å2-0 Å2
2---1.3 Å20 Å2
3---4.22 Å2
Refinement stepCycle: 1 / Resolution: 1.56→35.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 159 54 49 262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.014243
X-RAY DIFFRACTIONr_bond_other_d0.0040.02119
X-RAY DIFFRACTIONr_angle_refined_deg2.751.813383
X-RAY DIFFRACTIONr_angle_other_deg1.5373268
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_restr0.070.224
X-RAY DIFFRACTIONr_gen_planes_refined0.0270.02152
X-RAY DIFFRACTIONr_gen_planes_other0.0050.0267
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_it3.2962.667243
X-RAY DIFFRACTIONr_scbond_other3.29244
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2013.986384
X-RAY DIFFRACTIONr_long_range_B_refined4.0832.101647
X-RAY DIFFRACTIONr_long_range_B_other4.03732.626631
X-RAY DIFFRACTIONr_rigid_bond_restr3.2373243
X-RAY DIFFRACTIONr_sphericity_free33.076514
X-RAY DIFFRACTIONr_sphericity_bonded18.8625248
LS refinement shellResolution: 1.56→1.601 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 26 -
Rwork0.291 480 -
obs--98.64 %

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