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- PDB-5jev: del-[Ru(phen)2(dppz]2+ bound to d(TCGGCGCCGA) with Cobalt hexammine -

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Basic information

Entry
Database: PDB / ID: 5jev
Titledel-[Ru(phen)2(dppz]2+ bound to d(TCGGCGCCGA) with Cobalt hexammine
ComponentsDNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')
KeywordsDNA / Ruthenium / cross-linking / DNA probe
Function / homologyDelta-Ru(phen)2(dppz) complex / COBALT HEXAMMINE(III) / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.99 Å
AuthorsHall, J.P. / Cardin, C.J.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Delta chirality ruthenium 'light-switch' complexes can bind in the minor groove of DNA with five different binding modes.
Authors: Hall, J.P. / Keane, P.M. / Beer, H. / Buchner, K. / Winter, G. / Sorensen, T.L. / Cardin, D.J. / Brazier, J.A. / Cardin, C.J.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Nov 9, 2016Group: Database references
Revision 1.4May 8, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,6954
Polymers3,0461
Non-polymers1,6493
Water1,20767
1
A: DNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)9,3898
Polymers6,0922
Non-polymers3,2976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Unit cell
Length a, b, c (Å)48.720, 48.720, 29.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-221-

HOH

21A-267-

HOH

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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.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-0TN / Delta-Ru(phen)2(dppz) complex


Mass: 743.779 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H26N8Ru
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1uL 2mM d(TCGGCGCCGA), 1uL 2mM del-[Ru(phen)2(dppz)]2+, 6uL of a solution containing 10% (V/V) 2-methyl-2,4-pentanediol, 40mM Na-cacodylate, 20mM Cobalt hexammine, 12mM NaCl and 80mM KCl.

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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: Dec 14, 2012
RadiationMonochromator: dual Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 0.99→22.61 Å / Num. obs: 19226 / % possible obs: 94.1 % / Observed criterion σ(F): -3 / Redundancy: 6.5 % / CC1/2: 1 / Rmerge(I) obs: 0.031 / Net I/σ(I): 19.9
Reflection shellResolution: 0.99→1.02 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1.9 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
xia2data reduction
RefinementMethod to determine structure: SAD / Resolution: 0.99→18.901 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 12.52
RfactorNum. reflection% reflection
Rfree0.141 1804 5.22 %
Rwork0.1233 --
obs0.1242 19198 90.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.99→18.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 109 67 378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013475
X-RAY DIFFRACTIONf_angle_d2.325761
X-RAY DIFFRACTIONf_dihedral_angle_d27.801158
X-RAY DIFFRACTIONf_chiral_restr0.07658
X-RAY DIFFRACTIONf_plane_restr0.02121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.99-1.01680.25311350.2692545X-RAY DIFFRACTION91
1.0168-1.04670.22291590.23062498X-RAY DIFFRACTION90
1.0467-1.08050.18791580.18662499X-RAY DIFFRACTION90
1.0805-1.11910.17651360.15962556X-RAY DIFFRACTION91
1.1191-1.16390.13961630.12892512X-RAY DIFFRACTION91
1.1639-1.21680.1561480.11242572X-RAY DIFFRACTION91
1.2168-1.2810.11351280.09582526X-RAY DIFFRACTION90
1.281-1.36120.10741640.09222532X-RAY DIFFRACTION91
1.3612-1.46630.1041200.08592568X-RAY DIFFRACTION92
1.4663-1.61380.09981210.08192555X-RAY DIFFRACTION91
1.6138-1.84710.12371300.09172529X-RAY DIFFRACTION90
1.8471-2.32650.1411150.12892484X-RAY DIFFRACTION88
2.3265-18.90420.15331270.1422376X-RAY DIFFRACTION85

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