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- PDB-8edb: 5'-CGCGAATTCGCG-3' and an AT-specific binder (DB1884) complex -

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Basic information

Entry
Database: PDB / ID: 8edb
Title5'-CGCGAATTCGCG-3' and an AT-specific binder (DB1884) complex
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / SMALL MOLECULE / MINOR GROOVE
Function / homology4,4'-(1H-indole-2,6-diyl)dibenzenecarboximidamide / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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
DepositionSep 3, 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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-polymers3782
Water1,946108
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)25.770, 39.760, 65.350
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 the ligand DB1884.
Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-884 / 4,4'-(1H-indole-2,6-diyl)dibenzenecarboximidamide


Mass: 353.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19N5
#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.: 108 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, SODIUM CACODYLATE TRIHYDRATE, SPERMINE TETRAHYDROCHLORIDE, POTASSIUM CHLORIDE, MAGNESIUM CHLORIDE HEXAHYDRATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→25.24 Å / Num. obs: 10249 / % possible obs: 99.5 % / Redundancy: 2 % / CC1/2: 0.99 / Net I/σ(I): 17.92
Reflection shellResolution: 1.55→1.6 Å / Num. unique obs: 1004 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata scaling
XDSdata reduction
autoPROCdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IBNA

Resolution: 1.55→25.24 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 1019 9.99 %
Rwork0.1997 9183 -
obs0.2012 10202 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.08 Å2 / Biso mean: 24.2403 Å2 / Biso min: 12.23 Å2
Refinement stepCycle: final / Resolution: 1.55→25.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 49 108 643
Biso mean--29.99 33.03 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013574
X-RAY DIFFRACTIONf_angle_d1.521879
X-RAY DIFFRACTIONf_dihedral_angle_d29.4089258
X-RAY DIFFRACTIONf_chiral_restr0.07994
X-RAY DIFFRACTIONf_plane_restr0.01829
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B232X-RAY DIFFRACTION8.555TORSIONAL
12C232X-RAY DIFFRACTION8.555TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.630.31761400.26611279141999
1.63-1.730.21911410.2251269141099
1.73-1.870.25021430.205812881431100
1.87-2.060.25571450.227413011446100
2.06-2.350.25241480.210713261474100
2.35-2.960.23581470.220313271474100
2.97-25.240.17821550.17341393154899

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