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- PDB-4re7: Lambda-[Ru(TAP)2(dppz)]2+ bound to d(TCIGCGCCGA) -

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Basic information

Entry
Database: PDB / ID: 4re7
TitleLambda-[Ru(TAP)2(dppz)]2+ bound to d(TCIGCGCCGA)
Components5'-D(*TP*CP*IP*GP*CP*GP*CP*CP*GP*A)-3'
KeywordsDNA / inosine / kinking / ruthenium
Function / homology: / Ru(tap)2(dppz) complex / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.181 Å
AuthorsHall, J.P. / Cardin, C.J.
CitationJournal: To be Published
Title: The effects of DNA modification on the binding of polypyridyl ruthenium complexes
Authors: Hall, J.P. / Gurung, S.P. / Beer, H. / Buchner, K. / Cardin, D.J. / Brazier, J.A. / Cardin, C.J.
History
DepositionSep 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
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 / 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_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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Assembly

Deposited unit
A: 5'-D(*TP*CP*IP*GP*CP*GP*CP*CP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9163
Polymers3,0311
Non-polymers8852
Water181
1
A: 5'-D(*TP*CP*IP*GP*CP*GP*CP*CP*GP*A)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)7,8326
Polymers6,0622
Non-polymers1,7704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-11
Buried area1930 Å2
ΔGint-23 kcal/mol
Surface area4940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.830, 47.830, 32.110
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*IP*GP*CP*GP*CP*CP*GP*A)-3'


Mass: 3030.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-RKL / Ru(tap)2(dppz) complex


Mass: 747.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H22N12Ru
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1 uL 2 mM oligonucleotide (double HPLC-purified) + 1 uL 2 mM lambda-[Ru(TAP)2(dppz)]Cl2 + 6 uL 10% v/v MPD, 40 mM sodium cacodylate, pH 6.0, 12 mM spermine tetrahydrochloride, 80 mM sodium ...Details: 1 uL 2 mM oligonucleotide (double HPLC-purified) + 1 uL 2 mM lambda-[Ru(TAP)2(dppz)]Cl2 + 6 uL 10% v/v MPD, 40 mM sodium cacodylate, pH 6.0, 12 mM spermine tetrahydrochloride, 80 mM sodium chloride, 20 mM barium chloride equilibrated against 1 mL 35% v/v MPD, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.18→47.83 Å / Num. all: 2012 / Num. obs: 2012 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 11.5
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.122 / Mean I/σ(I) obs: 1.9 / % possible all: 93

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Processing

Software
NameVersionClassification
GDAdata collection
SHELXCDphasing
SHELXEmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.181→33.821 Å / SU ML: 0.22 / σ(F): 1.94 / Phase error: 45.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 159 4.57 %RANDOM
Rwork0.1925 ---
obs0.195 2000 93.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.181→33.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 201 52 1 254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005289
X-RAY DIFFRACTIONf_angle_d1.915454
X-RAY DIFFRACTIONf_dihedral_angle_d28.04897
X-RAY DIFFRACTIONf_chiral_restr0.02738
X-RAY DIFFRACTIONf_plane_restr0.00213
LS refinement shellResolution: 2.181→33.825 Å
RfactorNum. reflection% reflection
Rfree0.2417 159 -
Rwork0.1925 3318 -
obs--93 %
Refinement TLS params.Method: refined / Origin x: 10.5399 Å / Origin y: 11.9227 Å / Origin z: -19.6956 Å
111213212223313233
T0.7892 Å20.0531 Å2-0.0091 Å2-0.7835 Å2-0.0285 Å2--0.5859 Å2
L4.9133 °2-2.1317 °22.0699 °2-6.1569 °2-2.6301 °2--1.8969 °2
S-0.0704 Å °0.2214 Å °-0.732 Å °-0.3011 Å °0.2186 Å °0.1891 Å °-0.2632 Å °-0.1487 Å °-0.0333 Å °
Refinement TLS groupSelection details: chain 'A'

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