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- PDB-2htt: Ruthenium Hexammine ion interactions with Z-DNA -

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Basic information

Entry
Database: PDB / ID: 2htt
TitleRuthenium Hexammine ion interactions with Z-DNA
Components
  • DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DA)-3')
  • DNA (5'-D(*DTP*DGP*DCP*DGP*DCP*DG)-3')
  • DNA (5'-D(P*DTP*DG)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX
Function / homologyRUTHENIUM (III) HEXAAMINE ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBharanidharan, D. / Thiyagarajan, S. / Gautham, N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Hexammineruthenium(III) ion interactions with Z-DNA
Authors: Bharanidharan, D. / Thiyagarajan, S. / Gautham, N.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*DTP*DGP*DCP*DGP*DCP*DG)-3')
B: DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DA)-3')
D: DNA (5'-D(P*DTP*DG)-3')
E: DNA (5'-D(P*DTP*DG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0005
Polymers4,7964
Non-polymers2031
Water21612
1
A: DNA (5'-D(*DTP*DGP*DCP*DGP*DCP*DG)-3')
B: DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DA)-3')


Theoretical massNumber of molelcules
Total (without water)3,6192
Polymers3,6192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-7 kcal/mol
Surface area2490 Å2
MethodPISA
2
D: DNA (5'-D(P*DTP*DG)-3')
E: DNA (5'-D(P*DTP*DG)-3')
hetero molecules

D: DNA (5'-D(P*DTP*DG)-3')
E: DNA (5'-D(P*DTP*DG)-3')
hetero molecules

D: DNA (5'-D(P*DTP*DG)-3')
E: DNA (5'-D(P*DTP*DG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1409
Polymers3,5316
Non-polymers6103
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z+1/31
crystal symmetry operation5_555y,-x+y,z+1/61
3
D: DNA (5'-D(P*DTP*DG)-3')
E: DNA (5'-D(P*DTP*DG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,3803
Polymers1,1772
Non-polymers2031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-5 kcal/mol
Surface area1170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.895, 35.895, 44.604
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: DNA chain DNA (5'-D(*DTP*DGP*DCP*DGP*DCP*DG)-3')


Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DA)-3')


Mass: 1794.206 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*DTP*DG)-3')


Mass: 588.441 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-NRU / RUTHENIUM (III) HEXAAMINE ION / HEXAAMINORUTHENIUM


Mass: 203.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H18N6Ru
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 1.72946 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: MPD, sodium cacodylate, ruthenium hexammine chloride, spermine, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3ruthenium hexammine chloride11
4spermine11
5H2O11
6MPD12
7sodium cacodylate12
8ruthenium hexammine chloride12
9H2O12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 25, 2005
RadiationMonochromator: NIL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→31.16 Å / Num. all: 1207 / Num. obs: 1207 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.43 % / Rmerge(I) obs: 0.0873 / Net I/σ(I): 4.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.45 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 1.6 / Num. unique all: 181 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
AUTOMARdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ENTRY ZD0014

Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.864 / SU B: 19.976 / SU ML: 0.425 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.609 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.36371 87 8.8 %RANDOM
Rwork0.2579 ---
all0.295 989 --
obs0.26665 902 96.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.391 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 324 7 12 343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021366
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1413563
X-RAY DIFFRACTIONr_angle_other_deg
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_restr0.0750.262
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02167
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.2154
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.2180
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.26
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_scbond_it1.0753539
X-RAY DIFFRACTIONr_scangle_it1.8854.5560
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.01 4 -
Rwork0.358 59 -
obs--98.44 %

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