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- PDB-3uyb: X-ray crystal structure of the ruthenium complex [Ru(tap)2(dppz)]... -

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Basic information

Entry
Database: PDB / ID: 3uyb
TitleX-ray crystal structure of the ruthenium complex [Ru(tap)2(dppz)]2+ bound to d(TCGGTACCGA)
Components5'-D(*TP*CP*GP*GP*TP*AP*CP*CP*GP*A)-3'
KeywordsDNA / DNA-Ruthenium complex / Semiintercalation / intercalation / Minor groove interaction
Function / homology: / Ru(tap)2(dppz) complex / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsNiyazi, H.N. / Texeira, S.C.M. / Mitchell, E.P. / Cardin, J.C. / Forsyth, V.T.
CitationJournal: To be Published
Title: Crystal structure of lambda-[Ru(TAP)2(dppz)]2+ with d(TCGGTACCGA)2 displaying kinking of DNA via semiintercalation.
Authors: Niyazi, H.N. / O'Sullivan, K. / Texeira, S.C.M. / Mitchell, E.P. / Kelly, J.M. / Cardin, J.C. / Forsyth, V.T.
History
DepositionDec 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
SupersessionApr 29, 2015ID: 3UYA
Revision 1.1Apr 29, 2015Group: Other
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Mar 20, 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 / 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: 5'-D(*TP*CP*GP*GP*TP*AP*CP*CP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6784
Polymers3,0451
Non-polymers1,6333
Water1,18966
1
A: 5'-D(*TP*CP*GP*GP*TP*AP*CP*CP*GP*A)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)9,3568
Polymers6,0902
Non-polymers3,2666
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area950 Å2
ΔGint-5 kcal/mol
Surface area4630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.376, 54.376, 28.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain 5'-D(*TP*CP*GP*GP*TP*AP*CP*CP*GP*A)-3'


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-RKL / Ru(tap)2(dppz) complex


Mass: 747.732 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.52 Å3/Da / Density % sol: 65.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10%(v/v) 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM sodium chloride, 20mM barium chloride, 1mM DNA d(TCGGTACCGA), 1mM lambda-[Ru(tap)2dppz)Cl2 , pH 7.0, ...Details: 10%(v/v) 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM sodium chloride, 20mM barium chloride, 1mM DNA d(TCGGTACCGA), 1mM lambda-[Ru(tap)2dppz)Cl2 , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.5→38.45 Å / Num. obs: 7382 / % possible obs: 99.9 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7
Reflection shellResolution: 1.5→1.58 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHELXCDphasing
SHELXEmodel building
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→38.45 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.074 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 1.7 / ESU R: 0.068 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16672 316 4.6 %RANDOM
Rwork0.1267 ---
obs0.12859 6591 93.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.742 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0 Å2
2---0.06 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.5→38.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 103 66 371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.014360
X-RAY DIFFRACTIONr_angle_refined_deg3.5371.993576
X-RAY DIFFRACTIONr_chiral_restr0.0840.231
X-RAY DIFFRACTIONr_gen_planes_refined0.0380.02211
X-RAY DIFFRACTIONr_rigid_bond_restr9.6123360
X-RAY DIFFRACTIONr_sphericity_free25.876516
X-RAY DIFFRACTIONr_sphericity_bonded13.7775360
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 13 -
Rwork0.136 365 -
obs--79.41 %
Refinement TLS params.Method: refined / Origin x: -42.417 Å / Origin y: -39.996 Å / Origin z: 16.947 Å
111213212223313233
T0.0093 Å20.0022 Å20.0022 Å2-0.0075 Å20.0026 Å2--0.0013 Å2
L0.0001 °2-0.0001 °20.0001 °2-0.0002 °20.0001 °2--0.0002 °2
S-0.001 Å °-0.0004 Å °-0.0003 Å °0.0004 Å °0.001 Å °0.0004 Å °-0.0009 Å °0.0007 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 10
2X-RAY DIFFRACTION1A11 - 13
3X-RAY DIFFRACTION1A14 - 87

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