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- PDB-4e7y: Lambda-[Ru(phen)2(dppz)]2+ Bound to CCGGATCCGG -

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Basic information

Entry
Database: PDB / ID: 4e7y
TitleLambda-[Ru(phen)2(dppz)]2+ Bound to CCGGATCCGG
Components5'-D(*CP*CP*GP*GP*AP*TP*CP*CP*GP*G)-3'
KeywordsDNA / Intercalation / Lambda-[Ru(phen)2(dppz)]2+
Function / homology: / Lambda-Ru(phen)2(dppz) complex / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsHall, J.P. / Cardin, C.J.
CitationJournal: Nat Chem / Year: 2012
Title: Crystal Structure of lambda-[Ru(phen)2(dppz)]2+ with oligonucleotides containing TA/TA and AT/AT steps show two intercalation modes.
Authors: Niyazi, H. / Hall, J.P. / O'Sullivan, K. / Winter, G. / Sorensen, T. / Kelly, J.M. / Cardin, C.J.
History
DepositionMar 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Non-polymer description
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 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_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_conn.ptnr2_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,9273
Polymers3,0461
Non-polymers8812
Water95553
1
A: 5'-D(*CP*CP*GP*GP*AP*TP*CP*CP*GP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)7,8546
Polymers6,0922
Non-polymers1,7624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area900 Å2
ΔGint-5 kcal/mol
Surface area4400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.720, 47.720, 34.660
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-225-

HOH

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Components

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


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Purchased from ATDBio
#2: Chemical ChemComp-RKP / Lambda-Ru(phen)2(dppz) complex


Mass: 743.779 Da / Num. of mol.: 1 / 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


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.24 Å3/Da / Density % sol: 62.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1ul 2mM DNA Oligomer, 1ul 3mM Lambda-[Ru(phen)2(dppz)]2+, 1ul 1mM Lambda-[Ru(tap)2(dppz-(Me)2]2+, 6ul 10% 1-methyl-2,4-pentanediol, 40mM Sodium cacodylate, 12mM Spermeine tetra-HCl, 80mM ...Details: 1ul 2mM DNA Oligomer, 1ul 3mM Lambda-[Ru(phen)2(dppz)]2+, 1ul 1mM Lambda-[Ru(tap)2(dppz-(Me)2]2+, 6ul 10% 1-methyl-2,4-pentanediol, 40mM Sodium cacodylate, 12mM Spermeine tetra-HCl, 80mM Potassium Chloride, 20mM Barium Chloride, equilibrated against 1ml 35% 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2012
RadiationMonochromator: Si(111) dual crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→34.66 Å / Num. all: 4747 / Num. obs: 4747 / % possible obs: 100 %
Reflection shellResolution: 1.7→1.75 Å / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
SHELXCDphasing
SHELXEmodel building
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→33.74 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.737 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18837 216 4.6 %RANDOM
Rwork0.1553 ---
all0.1553 4596 --
obs0.15683 4506 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.951 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0 Å2-0 Å2
2---0.85 Å2-0 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 52 53 307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.013290
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.521.74456
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_restr0.1330.232
X-RAY DIFFRACTIONr_gen_planes_refined0.0380.02157
X-RAY DIFFRACTIONr_gen_planes_other
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 12 -
Rwork0.199 270 -
obs--99.65 %

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