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- PDB-7kwk: DNA-DB1879 complex: The DNA sequence 5'-CGCGAATTCGCG-3' presents ... -

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Basic information

Entry
Database: PDB / ID: 7kwk
TitleDNA-DB1879 complex: The DNA sequence 5'-CGCGAATTCGCG-3' presents a binding site for the heterocyclic small molecule (DB1879).
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA
Function / homologyChem-X8V / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsOgbonna, E. / Fang, Z. / Wilson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111749 United States
CitationJournal: Bioorg.Med.Chem. / Year: 2022
Title: Drug design and DNA structural research inspired by the Neidle laboratory: DNA minor groove binding and transcription factor inhibition by thiophene diamidines.
Authors: Ogbonna, E.N. / Paul, A. / Ross Terrell, J. / Fang, Z. / Chen, C. / Poon, G.M.K. / Boykin, D.W. / Wilson, W.D.
History
DepositionDec 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jun 29, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / entity / entity_poly / entity_poly_seq / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _ndb_struct_na_base_pair.i_label_seq_id / _ndb_struct_na_base_pair.j_label_seq_id / _ndb_struct_na_base_pair_step.i_label_seq_id_1 / _ndb_struct_na_base_pair_step.i_label_seq_id_2 / _ndb_struct_na_base_pair_step.j_label_seq_id_1 / _ndb_struct_na_base_pair_step.j_label_seq_id_2 / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.seq_align_end
Revision 2.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: 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)7,7114
Polymers7,3272
Non-polymers3842
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-5 kcal/mol
Surface area4400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.912, 39.945, 65.143
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-X8V / 2-[5-(4-carbamimidoylphenyl)thiophen-2-yl]-1H-indole-6-carboximidamide


Mass: 359.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17N5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% MPD, 0.04M Sodium Cacodylate trihydrate, 0.02M Hexamine Cobalt(III) Chloride, Magnesium Chloride hexahydrate
Temp details: Temperature was kept constant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.14 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 28, 2020
RadiationMonochromator: SINGLE CRYSTAL Si(200) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. obs: 14801 / % possible obs: 99.6 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.015 / Rrim(I) all: 0.053 / Χ2: 0.97 / Net I/σ(I): 13.4 / Num. measured all: 179467
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.37-1.399.70.56810.9390.1610.5260.7295
1.39-1.4210.80.4487120.9560.1350.4690.75597.9
1.42-1.4511.40.3917240.9750.1160.4090.8199
1.45-1.48120.3437180.9790.1020.3580.823100
1.48-1.5111.90.2987120.980.0880.3110.924100
1.51-1.5412.50.2527500.9840.0730.2630.978100
1.54-1.5812.10.2117110.990.0620.221.197100
1.58-1.6212.80.1517450.9970.0430.1571.212100
1.62-1.6712.70.1317310.9970.0370.1371.268100
1.67-1.7312.50.1337400.9960.0390.1391.42100
1.73-1.7912.20.1267180.9970.0370.1321.42100
1.79-1.8612.60.1227540.9960.0350.1271.393100
1.86-1.9412.70.1127260.9960.0330.1171.295100
1.94-2.05130.1037470.9970.0290.1071.158100
2.05-2.1712.50.0967490.9970.0280.11.064100
2.17-2.3412.40.0847540.9970.0250.0880.894100
2.34-2.5812.50.0767470.9980.0220.0790.75100
2.58-2.9512.70.0647640.9990.0180.0670.569100
2.95-3.7211.90.0417790.9990.0120.0430.39299.9
3.72-5011.50.0418390.9990.0120.0430.27699.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000v721data scaling
PDB_EXTRACT3.27data extraction
HKL-2000v721data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BNA

1bna


Resolution: 1.37→34.05 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 1.104 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2637 670 5 %RANDOM
Rwork0.2207 ---
obs0.2227 12812 90.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 35 Å2 / Biso mean: 13.418 Å2 / Biso min: 5.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.37→34.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 27 80 593
Biso mean--18.63 22.63 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.011573
X-RAY DIFFRACTIONr_bond_other_d0.0030.02289
X-RAY DIFFRACTIONr_angle_refined_deg2.0451.251878
X-RAY DIFFRACTIONr_angle_other_deg1.6333.03672
X-RAY DIFFRACTIONr_chiral_restr0.0750.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0350.02326
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021147
LS refinement shellResolution: 1.37→1.405 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.323 31 -
Rwork0.278 558 -
obs--55.94 %

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