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- PDB-4ly2: X-ray crystal structure of the ruthenium complex [Ru(phen)2(dppz)... -

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Basic information

Entry
Database: PDB / ID: 4ly2
TitleX-ray crystal structure of the ruthenium complex [Ru(phen)2(dppz)]2+ bound to d(TCGGTACCGA)
ComponentsDNA
KeywordsDNA / Intercalation / semi-intercalation / symmetrical intercalation / ligand binding / Light-switch compounds / DNA damage agent / guanine oxidation
Function / homology: / Lambda-Ru(phen)2(dppz) complex / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 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(phen)2(dppz)]2+ bound to d(TCGGTACCGA)
Authors: Niyazi, H. / Teixeira, S. / Mitchell, E. / Forsyth, T. / Cardin, C.
History
DepositionJul 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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)4,6704
Polymers3,0451
Non-polymers1,6253
Water36020
1
A: DNA
hetero molecules

A: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3408
Polymers6,0902
Non-polymers3,2506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area930 Å2
ΔGint-5 kcal/mol
Surface area4600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.450, 52.450, 32.580
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-

RKP

21A-217-

HOH

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Components

#1: DNA chain DNA /


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA purchased from ATDbio Ltd
#2: Chemical ChemComp-RKP / Lambda-Ru(phen)2(dppz) complex


Mass: 743.779 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H26N8Ru
#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.: 20 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Performed using the sitting drop vapour diffusion method, by adding 1ul (4mM) L-[Ru(phen)2(dppz)]2+ to a drop containing 1ul (1mM) d(TCGGTACCGA)2, and 8ul of a solution containing 12mM ...Details: Performed using the sitting drop vapour diffusion method, by adding 1ul (4mM) L-[Ru(phen)2(dppz)]2+ to a drop containing 1ul (1mM) d(TCGGTACCGA)2, and 8ul of a solution containing 12mM spermine, 10% 2-methyl-2,4-pentanediol, 40 mM sodium cacodylate pH 7.0, 80 mM NaCl and 20 mM BaCl2. This was equilibrated against 1 ml of 35% 2-methyl-2,4-pantanediol at room temperature, 20 C., 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: 1.54980, 0.97240
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2012
RadiationMonochromator: Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54981
20.97241
ReflectionResolution: 1.76→52.45 Å / Num. obs: 4849 / % possible obs: 98.8 % / 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: MAD / Resolution: 2.1→37.09 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.391 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 129 4.5 %RANDOM
Rwork0.18817 ---
obs0.18968 2711 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0 Å2-0 Å2
2---0.6 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 103 20 325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.014354
X-RAY DIFFRACTIONr_bond_other_d0.0030.02171
X-RAY DIFFRACTIONr_angle_refined_deg3.3481.873565
X-RAY DIFFRACTIONr_angle_other_deg3.3513389
X-RAY DIFFRACTIONr_chiral_restr0.8840.238
X-RAY DIFFRACTIONr_gen_planes_refined0.0320.02225
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02104
LS refinement shellResolution: 2.099→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.187 5 -
Rwork0.24 178 -
obs--88.41 %

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