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- PDB-4m3i: X-ray crystal structure of the ruthenium complex [Ru(TAP)2(dppz-{... -

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Basic information

Entry
Database: PDB / ID: 4m3i
TitleX-ray crystal structure of the ruthenium complex [Ru(TAP)2(dppz-{Me2})]2+ bound to d(CCGGTACCGG)
ComponentsSynthetic DNA CCGGTACCGG
KeywordsDNA / Intercalation / Semi-intercalation / minor-groove binder / light-switch / bending / kinking
Function / homology: / Chem-RML / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsNiyazi, H. / Teixeira, S. / Mitchell, E. / Forsyth, T. / Cardin, C.
CitationJournal: To be Published
Title: X-ray crystal structure of the ruthenium complex [Ru(TAP)2(dppz-{Me2})]2+ bound to d(CCGGTACCGG)
Authors: Niyazi, H. / Teixeira, S. / Mitchell, E. / Forsyth, T. / Cardin, C.
History
DepositionAug 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synthetic DNA CCGGTACCGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7354
Polymers3,0461
Non-polymers1,6893
Water23413
1
A: Synthetic DNA CCGGTACCGG
hetero molecules

A: Synthetic DNA CCGGTACCGG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4708
Polymers6,0922
Non-polymers3,3786
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area970 Å2
ΔGint-6 kcal/mol
Surface area4490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.279, 53.279, 33.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-102-

RML

21A-102-

RML

31A-208-

HOH

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Components

#1: DNA chain Synthetic DNA CCGGTACCGG


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Purchased Synthetic Construct
#2: Chemical ChemComp-RML / (11,12-dimethyldipyrido[3,2-a:2',3'-c]phenazine-kappa~2~N~4~,N~5~)[bis(pyrazino[2,3-f]quinoxaline-kappa~2~N~1~,N~10~)]ruthenium(2+) / Lambda-[Ru(1,4,5,8-tetraazaphenanthrene)2(11,12-dimethyl-dipyridophenazine)]2+


Mass: 775.785 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H26N12Ru
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.93 Å3/Da / Density % sol: 68.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10ul drop containing 1ul of 4mM-[Ru(TAP)2(dppz-{Me2})]2+, 1ul of 1 mM d(CCGGTACCGG)2, and a 8ul addition containing 12mM spermine, 10% 2-methyl-2,4-pentanediol, 40mM sodium cacodylate pH 7. ...Details: 10ul drop containing 1ul of 4mM-[Ru(TAP)2(dppz-{Me2})]2+, 1ul of 1 mM d(CCGGTACCGG)2, and a 8ul addition containing 12mM spermine, 10% 2-methyl-2,4-pentanediol, 40mM sodium cacodylate pH 7.0, 80mM NaCl and 20mM BaCl2. This was equilibrated against 1ml of 35% 2-methyl-,4-pantanediol. , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→53.28 Å / Num. obs: 3114 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHELXSphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→37.67 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.111 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27743 129 4.4 %RANDOM
Rwork0.25147 ---
obs0.25266 2774 93.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.991 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å20 Å20 Å2
2--2.73 Å20 Å2
3----5.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 198 107 13 318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.014353
X-RAY DIFFRACTIONr_bond_other_d0.0080.02162
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.893564
X-RAY DIFFRACTIONr_angle_other_deg2.683363
X-RAY DIFFRACTIONr_chiral_restr0.1490.233
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.02231
X-RAY DIFFRACTIONr_gen_planes_other0.0210.0294
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 11 -
Rwork0.344 180 -
obs--89.25 %

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