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- PDB-6rso: Structure of [Ru(phen)2(10-NO2-dppz)]2+ bound to the DNA sequence... -

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Basic information

Entry
Database: PDB / ID: 6rso
TitleStructure of [Ru(phen)2(10-NO2-dppz)]2+ bound to the DNA sequence d(TCGGCGCCGA)
ComponentsDNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')
KeywordsDNA / Ruthenium / intercalation / asymmetric
Function / homology: / Chem-KHN / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 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: Structure of [Ru(phen)2(10-NO2-dppz)]2+ bound to the DNA sequence d(TCGGCGCCGA)
Authors: McQuaid, K.T. / Hall, J.P. / Cardin, C.J.
History
DepositionMay 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Derived calculations / Structure summary / Category: pdbx_struct_conn_angle / struct / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._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.title / _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
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_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)7,9466
Polymers6,0922
Non-polymers1,8544
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-26 kcal/mol
Surface area4400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.730, 46.730, 31.990
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-KHN / Ruthenium (bis-(phenanthroline)) (10-nitro-dipyridophenazine)


Mass: 789.785 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H26N9O2Ru / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.87 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 8 uL drop containing; 250 uM d(TCGGCGCCGA), 625 uM rac-[Ru(phen)2(10-NO2-dppz)]Cl2, 7.5% v/v MPD, 30 mM pH 7 sodium cacodylate, 9 mM spermine tetrahydrochloride, 60 mM KCl and 15 mM BaCl2, ...Details: 8 uL drop containing; 250 uM d(TCGGCGCCGA), 625 uM rac-[Ru(phen)2(10-NO2-dppz)]Cl2, 7.5% v/v MPD, 30 mM pH 7 sodium cacodylate, 9 mM spermine tetrahydrochloride, 60 mM KCl and 15 mM BaCl2, all equilibrated against 500 uL of 35% v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.97→46.73 Å / Num. obs: 9539 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.014 / Rrim(I) all: 0.051 / Net I/σ(I): 26.9
Reflection shellResolution: 1.97→2 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 246 / CC1/2: 0.334 / Rpim(I) all: 0.804 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.15rc2_3433: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.97→26.397 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 511 5.36 %Random Selection
Rwork0.2068 ---
obs0.209 9533 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→26.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 110 30 544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008586
X-RAY DIFFRACTIONf_angle_d0.868922
X-RAY DIFFRACTIONf_dihedral_angle_d23.928204
X-RAY DIFFRACTIONf_chiral_restr0.03978
X-RAY DIFFRACTIONf_plane_restr0.00828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9701-2.16830.40231040.3142266X-RAY DIFFRACTION100
2.1683-2.48180.23361600.21452264X-RAY DIFFRACTION100
2.4818-3.1260.32091160.26712231X-RAY DIFFRACTION100
3.126-26.39950.22711310.18412261X-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)
15.9744-5.6343-7.73717.31465.02675.2555-0.0381-0.441-0.04590.0787-0.20730.3346-0.0285-0.51630.29940.51870.05860.03390.73860.05690.625611.6243-10.54643.1156
25.0786-6.3327-4.39735.90217.1765.1412-0.18070.1995-0.2511-0.47270.0082-0.04070.4396-0.10390.05690.78820.0357-0.05720.6017-0.06060.656712.7985-11.746-4.0657
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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