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- PDB-4e1u: [Ru(bpy)2 dppz]2+ bound to DNA -

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Basic information

Entry
Database: PDB / ID: 4e1u
Title[Ru(bpy)2 dppz]2+ bound to DNA
Components5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*AP*CP*CP*G)-3'
KeywordsDNA / Mismatch / Small molecule
Function / homology: / Delta-[Ru(bpy)2dppz]2+ / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.92 Å
AuthorsSong, H. / Kaiser, J.T. / Barton, J.K.
CitationJournal: Nat Chem / Year: 2012
Title: Crystal structure of delta-[Ru(bpy)2dppz]2+ bound to mismatched DNA reveals side-by-side metalloinsertion and intercalation.
Authors: Song, H. / Kaiser, J.T. / Barton, J.K.
History
DepositionMar 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Non-polymer description
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Feb 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,0969
Polymers7,3432
Non-polymers3,7537
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-5 kcal/mol
Surface area5510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.039, 24.797, 37.521
Angle α, β, γ (deg.)74.67, 84.42, 76.21
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 3671.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Engineered mismatch
#2: Chemical
ChemComp-R1Z / Delta-[Ru(bpy)2dppz]2+


Mass: 695.737 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C38H26N8Ru
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 7
Details: 20mM Cacodylate; 6mM Spermine*HCl; 40mM NaCl; 10mM BaCl2 5% 2-M-2,4PD, pH 7.0, VAPOR DIFFUSION, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 0.92→36 Å / Num. obs: 46920 / % possible obs: 82.7 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.03 / Rsym value: 0.03 / Net I/σ(I): 20

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHELXDphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 0.92→23.33 Å / SU ML: 0.1 / σ(F): 1.98 / Phase error: 15.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.149 4695 5.1 %
Rwork0.1397 --
obs0.1401 46920 81.74 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.295 Å2 / ksol: 0.439 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2315 Å2-1.9032 Å20.7312 Å2
2--1.5877 Å20.3666 Å2
3----1.3562 Å2
Refinement stepCycle: LAST / Resolution: 0.92→23.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 488 237 197 922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111050
X-RAY DIFFRACTIONf_angle_d1.621572
X-RAY DIFFRACTIONf_dihedral_angle_d34.206338
X-RAY DIFFRACTIONf_chiral_restr0.074134
X-RAY DIFFRACTIONf_plane_restr0.01759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.92-0.93050.3264880.28661572X-RAY DIFFRACTION45
0.9305-0.94140.2911160.26972133X-RAY DIFFRACTION60
0.9414-0.95290.29691430.26422743X-RAY DIFFRACTION75
0.9529-0.9650.27561490.25042817X-RAY DIFFRACTION80
0.965-0.97770.23121420.21572890X-RAY DIFFRACTION81
0.9777-0.99110.26291570.20462956X-RAY DIFFRACTION82
0.9911-1.00520.22181460.19552834X-RAY DIFFRACTION80
1.0052-1.02020.21751560.18242788X-RAY DIFFRACTION81
1.0202-1.03620.19641310.18022910X-RAY DIFFRACTION78
1.0362-1.05320.19481560.16642721X-RAY DIFFRACTION79
1.0532-1.07130.1821560.1533082X-RAY DIFFRACTION85
1.0713-1.09080.16121560.1473040X-RAY DIFFRACTION85
1.0908-1.11180.15221730.14093029X-RAY DIFFRACTION87
1.1118-1.13450.17461650.13543079X-RAY DIFFRACTION85
1.1345-1.15920.14431920.12972952X-RAY DIFFRACTION84
1.1592-1.18610.15071740.12532895X-RAY DIFFRACTION82
1.1861-1.21580.13981500.12342681X-RAY DIFFRACTION76
1.2158-1.24870.12761700.11963184X-RAY DIFFRACTION88
1.2487-1.28540.14671570.11413076X-RAY DIFFRACTION87
1.2854-1.32690.11952040.10623108X-RAY DIFFRACTION88
1.3269-1.37430.13211670.10733142X-RAY DIFFRACTION88
1.3743-1.42930.13511530.10733130X-RAY DIFFRACTION87
1.4293-1.49440.13241900.10422856X-RAY DIFFRACTION81
1.4944-1.57310.12861450.1153048X-RAY DIFFRACTION85
1.5731-1.67170.11221720.11973226X-RAY DIFFRACTION90
1.6717-1.80070.13571710.12373103X-RAY DIFFRACTION88
1.8007-1.98180.15021220.13193153X-RAY DIFFRACTION87
1.9818-2.26840.15211420.1392904X-RAY DIFFRACTION81
2.2684-2.85710.15531970.16043157X-RAY DIFFRACTION90
2.8571-23.33780.14941550.15243110X-RAY DIFFRACTION86

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