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- PDB-4ltk: Dehydration/Rehydration of a Nucleic Acid system containing a Pol... -

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Basic information

Entry
Database: PDB / ID: 4ltk
TitleDehydration/Rehydration of a Nucleic Acid system containing a Polypyridyl Ruthenium Complex at 74% relative humidity (6/7)
ComponentsDNA
KeywordsDNA / Dehydration / HC1b / Kinking / ruthenium
Function / homology: / Ru(tap)2(dppz) complex / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHall, J.P. / Sanchez-Weatherby, J. / Cardin, C.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Controlled Dehydration of a Ruthenium Complex-DNA Crystal Induces Reversible DNA Kinking.
Authors: Hall, J.P. / Sanchez-Weatherby, J. / Alberti, C. / Quimper, C.H. / O'Sullivan, K. / Brazier, J.A. / Winter, G. / Sorensen, T. / Kelly, J.M. / Cardin, D.J. / Cardin, C.J.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Jan 7, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_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_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_conn.pdbx_dist_value / _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_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 / _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

Downloads & links

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Assembly

Deposited unit
A: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9674
Polymers3,0461
Non-polymers9213
Water55831
1
A: DNA
hetero molecules

A: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9338
Polymers6,0922
Non-polymers1,8416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Buried area1970 Å2
ΔGint-55 kcal/mol
Surface area4750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.150, 44.150, 27.490
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-103-

CL

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Components

#1: DNA chain DNA


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesised by ATDBio
#2: Chemical ChemComp-RKL / Ru(tap)2(dppz) complex


Mass: 747.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H22N12Ru
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#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.: 31 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 1ul 1mM d(TCGGCGCCGA)2, 1ul 4mM lambda-[Ru(TAP)2(dppz)]2+, 6ul 12mM spermine, 10% MPD, 40mM sodium cacodylate, 80mM KCl, 20mM BaCl2. Equilibriated against 1ml 35% MPD. Crystal was dehydrated ...Details: 1ul 1mM d(TCGGCGCCGA)2, 1ul 4mM lambda-[Ru(TAP)2(dppz)]2+, 6ul 12mM spermine, 10% MPD, 40mM sodium cacodylate, 80mM KCl, 20mM BaCl2. Equilibriated against 1ml 35% MPD. Crystal was dehydrated to 74% relative humidity on the beamline using the HC1b., pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.8266 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 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: 1.45→27.49 Å / Num. all: 5180 / Num. obs: 5810 / % possible obs: 99.9 % / Observed criterion σ(I): 2.6
Reflection shellResolution: 1.45→1.49 Å / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S80

3s80
PDB Unreleased entry


Resolution: 1.45→23.35 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.942 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15352 238 4.6 %RANDOM
Rwork0.13609 ---
obs0.13685 4913 99.9 %-
all-4913 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.541 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å2-0 Å2
2--0.13 Å2-0 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.45→23.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 53 31 286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.013290
X-RAY DIFFRACTIONr_bond_other_d0.0020.02134
X-RAY DIFFRACTIONr_angle_refined_deg2.8931.598456
X-RAY DIFFRACTIONr_angle_other_deg1.6353308
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_restr0.0820.230
X-RAY DIFFRACTIONr_gen_planes_refined0.0380.02176
X-RAY DIFFRACTIONr_gen_planes_other0.0050.0278
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3311.963290
X-RAY DIFFRACTIONr_scbond_other2.3271.964291
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5582.932457
X-RAY DIFFRACTIONr_long_range_B_refined4.74120.843632
X-RAY DIFFRACTIONr_long_range_B_other4.73620.775625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 19 -
Rwork0.205 359 -
obs--100 %

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