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- PDB-5jeu: del-[Ru(phen)2(dppz)]2+ bound to d(TCGGCGCCGA) with Ba2+ -

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Basic information

Entry
Database: PDB / ID: 5jeu
Titledel-[Ru(phen)2(dppz)]2+ bound to d(TCGGCGCCGA) with Ba2+
ComponentsDNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')
KeywordsDNA / ruthenium / light-switch / semi-intercalation
Function / homologyDelta-Ru(phen)2(dppz) complex / : / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.97 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)4,7065
Polymers3,0461
Non-polymers1,6604
Water1,47782
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)9,41310
Polymers6,0922
Non-polymers3,3218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)48.620, 48.620, 29.430
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-232-

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-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-0TN / Delta-Ru(phen)2(dppz) complex


Mass: 743.779 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H26N8Ru
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.85 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1uL 4mM del-[Ru(phen)2(dppz)]2+, 1uL 2mM d(TCGGCGCCGA), 6uL of a solution containing 40mM Na-cacodylate pH 7, 12mM spermine, 80mM KCl, 20mM BaCl2, 10% (v/v) hexylene glycol

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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: 0.97→25.18 Å / Num. obs: 20581 / % possible obs: 96.7 % / Observed criterion σ(F): -3 / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.027 / Net I/σ(I): 25.3
Reflection shellResolution: 0.97→1 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.857 / Mean I/σ(I) obs: 1.9 / % possible all: 97.3

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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: 0.97→25.177 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 13.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1267 1905 4.97 %
Rwork0.1125 --
obs0.1133 38325 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.97→25.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 104 82 388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013373
X-RAY DIFFRACTIONf_angle_d2.525595
X-RAY DIFFRACTIONf_dihedral_angle_d28.643115
X-RAY DIFFRACTIONf_chiral_restr0.06742
X-RAY DIFFRACTIONf_plane_restr0.02817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9701-0.99430.27691450.26522660X-RAY DIFFRACTION97
0.9943-1.02120.27321470.24052628X-RAY DIFFRACTION98
1.0212-1.05130.23421330.20542680X-RAY DIFFRACTION98
1.0513-1.08520.18241240.18152649X-RAY DIFFRACTION98
1.0852-1.1240.17411580.15242592X-RAY DIFFRACTION98
1.124-1.1690.12451250.12692655X-RAY DIFFRACTION97
1.169-1.22220.12191510.11342587X-RAY DIFFRACTION97
1.2222-1.28660.10691260.09682635X-RAY DIFFRACTION96
1.2866-1.36720.09721310.08722538X-RAY DIFFRACTION95
1.3672-1.47280.08511400.08772581X-RAY DIFFRACTION94
1.4728-1.6210.08751240.08162566X-RAY DIFFRACTION94
1.621-1.85550.11451420.09162528X-RAY DIFFRACTION94
1.8555-2.33740.11281290.10712571X-RAY DIFFRACTION94
2.3374-25.18540.13711300.11462550X-RAY DIFFRACTION94

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