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- PDB-7ku4: DNA-DB818 complex: The DNA sequence 5'-CGCGAATTCGCG-3' presents a... -

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Basic information

Entry
Database: PDB / ID: 7ku4
TitleDNA-DB818 complex: The DNA sequence 5'-CGCGAATTCGCG-3' presents a binding site for the heterocyclic small molecule (DB818).
Components1:(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / DNA-molecule complex
Function / homologyChem-D1B / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsOgbonna, E. / Fang, Z. / 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: 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
DepositionNov 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 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 1.2Oct 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: 1:(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: 1:(5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7124
Polymers7,3272
Non-polymers3852
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-7 kcal/mol
Surface area4210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.335, 40.127, 65.451
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 1:(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-D1B / 2-(5-{4-[AMINO(IMINO)METHYL]PHENYL}-2-THIENYL)-1H-BENZIMIDAZOLE-6- CARBOXIMIDAMIDE DIHYDROCHLORIDE


Mass: 360.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16N6S / Feature type: SUBJECT OF INVESTIGATION
#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.: 73 / 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 meas: 0.717 Mg/m3 / Density % sol: 46.79 % / Description: Rod shaped crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% MPD, 0.040M Sodium Cacodylate trihydrate, 0.012 Spermine Tetrahydrate, 0.080M Sodium Chloride, 0.020M 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: 1.6→50 Å / Num. obs: 9102 / % possible obs: 96.6 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.021 / Rrim(I) all: 0.073 / Χ2: 0.981 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.6312.30.4934300.980.1460.5150.98395.1
1.63-1.6612.50.4394300.9850.1290.4581.03295.3
1.66-1.6912.30.3654450.9850.1080.3811.03794.7
1.69-1.72120.3024260.9880.0920.3161.07195.3
1.72-1.7611.50.2774470.9880.0840.291.10995.9
1.76-1.812.60.2614440.9750.0760.2721.15396.1
1.8-1.8512.30.2334430.9850.0690.2431.17395.7
1.85-1.911.70.2144300.9750.0660.2241.17395.8
1.9-1.9512.60.1954530.9880.0570.2031.18496.2
1.95-2.0212.70.1764520.980.0510.1841.1896.6
2.02-2.0912.60.1594470.9890.0470.1661.19596.5
2.09-2.1712.40.1474450.990.0420.1531.16596.7
2.17-2.2712.20.134600.9850.0380.1361.13996.6
2.27-2.3912.30.1184550.9940.0340.1231.03597.4
2.39-2.5412.40.1084670.9890.0320.1130.94296.9
2.54-2.7412.80.0924570.9970.0260.0950.84697.6
2.74-3.0112.20.0794620.9970.0240.0830.7597.9
3.01-3.4511.80.0684810.9970.0220.0720.59898.2
3.45-4.3412.10.0624980.9970.0190.0650.49598.6
4.34-5011.10.0525300.9990.0160.0550.46997.4

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Processing

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

1bna


Resolution: 1.6→34.21 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.75 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 446 5.3 %RANDOM
Rwork0.2168 ---
obs0.2176 8046 90.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 33.98 Å2 / Biso mean: 12.119 Å2 / Biso min: 4.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.6→34.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 27 73 586
Biso mean--19.61 20.73 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.011573
X-RAY DIFFRACTIONr_bond_other_d0.0030.02288
X-RAY DIFFRACTIONr_angle_refined_deg2.0571.251878
X-RAY DIFFRACTIONr_angle_other_deg1.6683.03670
X-RAY DIFFRACTIONr_chiral_restr0.0720.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0310.02326
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021146
LS refinement shellResolution: 1.6→1.636 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.123 21 -
Rwork0.192 339 -
all-360 -
obs--54.05 %

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