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- PDB-8ec1: 5'-CGCGAATTCGCG-3' and benzimidazole diamidine (DB1476) comlpex w... -

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Basic information

Entry
Database: PDB / ID: 8ec1
Title5'-CGCGAATTCGCG-3' and benzimidazole diamidine (DB1476) comlpex with ligand orientation I
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / MINOR GROOVE / SMALL MOLECULE
Function / homologyChem-WFB / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo (humans)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsOgbonna, E.N. / Wilson, W.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111749 United States
CitationJournal: Acs Bio Med Chem Au / Year: 2023
Title: X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences.
Authors: Ogbonna, E.N. / Paul, A. / Farahat, A.A. / Terrell, J.R. / Mineva, E. / Ogbonna, V. / Boykin, D.W. / Wilson, W.D.
History
DepositionAug 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,7054
Polymers7,3272
Non-polymers3792
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.792, 40.069, 65.554
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and resid 1 through 12)
21chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DC / Beg label comp-ID: DC / End auth comp-ID: DG / End label comp-ID: DG / Label seq-ID: 1 - 12

Dom-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1(chain B and resid 1 through 12)BA1 - 12
2chain CCB13 - 24

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Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: A self-complementary DNA (5'-CGCGAATTCGCG-3') bound by ligand (DB1476) in a type I orientation.
Source: (synth.) Homo (humans)
#2: Chemical ChemComp-WFB / 4,4'-(1H-benzimidazole-2,6-diyl)di(benzene-1-carboximidamide)


Mass: 354.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18N6
#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.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: magnesium chloride hexahydrate, sodium chloride, potassium chloride, double-stranded DNA, MPD ,spermine tetrahydrate, sodium cacodylate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.98 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 7, 2022
Details: Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror water
RadiationMonochromator: double crystal - water cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.63→34.2 Å / Num. obs: 8886 / % possible obs: 99 % / Redundancy: 1.2 % / CC1/2: 1 / Net I/σ(I): 21.7
Reflection shellResolution: 1.63→1.69 Å / Num. unique obs: 807 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROC3.27data processing
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BNA

1bna


Resolution: 1.63→34.19 Å / SU B: 25.89 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 0.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 885 10 %
Rwork0.1839 7968 -
obs0.1882 8886 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.89 Å2 / Biso mean: 28 Å2 / Biso min: 16.63 Å2
Refinement stepCycle: final / Resolution: 1.63→34.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 48 105 639
Biso mean--40.16 36.64 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011574
X-RAY DIFFRACTIONf_angle_d1.46879
X-RAY DIFFRACTIONf_dihedral_angle_d29.219258
X-RAY DIFFRACTIONf_chiral_restr0.07494
X-RAY DIFFRACTIONf_plane_restr0.01729
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B232X-RAY DIFFRACTION3.841TORSIONAL
12C232X-RAY DIFFRACTION3.841TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.63-1.730.30081360.2198124595
1.73-1.870.23581460.20091308100
1.87-2.050.25271460.20031315100
Refinement TLS params.Method: refined / Origin x: 14.7949 Å / Origin y: 20.9234 Å / Origin z: 9.0799 Å
111213212223313233
T0.213 Å2-0.0142 Å20.0191 Å2-0.1871 Å2-0.0037 Å2--0.2421 Å2
L0.7153 °20.078 °20.9509 °2-1.0907 °22.0131 °2--5.517 °2
S0.0566 Å °-0.0562 Å °0.0199 Å °-0.1387 Å °0.0738 Å °-0.068 Å °-0.3288 Å °-0.1353 Å °-0.1118 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB1 - 12
2X-RAY DIFFRACTION1allB101
3X-RAY DIFFRACTION1allC13 - 24
4X-RAY DIFFRACTION1allS2 - 111
5X-RAY DIFFRACTION1allA1

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