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- PDB-4z4b: 2-Pyridyl Hoechst - a New Generation DNA-Binding Radioprotector -

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Basic information

Entry
Database: PDB / ID: 4z4b
Title2-Pyridyl Hoechst - a New Generation DNA-Binding Radioprotector
ComponentsDNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')
KeywordsDNA / Hoechst
Function / homologyChem-4L1 / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9652 Å
AuthorsWee, J.-Y. / Dobson, R.C.J. / White, J.M.
CitationJournal: To Be Published
Title: 2-Pyridyl Hoechst - a New Generation DNA-Binding Radioprotector
Authors: Wee, J.-Y. / Dobson, R.C.J. / White, J.M.
History
DepositionApr 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,7594
Polymers7,3252
Non-polymers4342
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.858, 40.797, 64.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-4L1 / 5-(4-methylpiperazin-1-yl)-2'-(pyridin-2-yl)-1H,1'H-2,5'-bibenzimidazole


Mass: 409.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23N7
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The hanging drops contained the following constituents (final drop concentrations): DNA 0.63 mM, Ligand 1 0.63 mM, MgCl2 2.1 mM, spermine 1.05 mM, MPD 4.2%. MgCl2 and spermine were made in ...Details: The hanging drops contained the following constituents (final drop concentrations): DNA 0.63 mM, Ligand 1 0.63 mM, MgCl2 2.1 mM, spermine 1.05 mM, MPD 4.2%. MgCl2 and spermine were made in 30 mM sodium cacodylate buffer at pH 7.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9567 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9567 Å / Relative weight: 1
ReflectionResolution: 1.965→40.8 Å / Num. obs: 8900 / % possible obs: 98.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.8
Reflection shellResolution: 1.965→2.01 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 4.1 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unpublished model

Resolution: 1.9652→34.485 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 877 9.85 %
Rwork0.1684 --
obs0.1727 8900 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9652→34.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 32 67 585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01622
X-RAY DIFFRACTIONf_angle_d1.829955
X-RAY DIFFRACTIONf_dihedral_angle_d35.596276
X-RAY DIFFRACTIONf_chiral_restr0.05694
X-RAY DIFFRACTIONf_plane_restr0.00930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9652-2.08830.3291600.22671280X-RAY DIFFRACTION93
2.0883-2.24950.34171360.21421355X-RAY DIFFRACTION100
2.2495-2.47580.30241460.21451361X-RAY DIFFRACTION100
2.4758-2.83390.2481330.19891371X-RAY DIFFRACTION100
2.8339-3.56990.18531500.15731347X-RAY DIFFRACTION99
3.5699-34.490.16921520.14161309X-RAY DIFFRACTION97

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