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- PDB-9cjw: The 24mer DNA Duplex 5'-GCTGGAAAGTTTAAACTTTCCAGC-3' Bound by the ... -

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Basic information

Entry
Database: PDB / ID: 9cjw
TitleThe 24mer DNA Duplex 5'-GCTGGAAAGTTTAAACTTTCCAGC-3' Bound by the Diamidine DB2447 at Single G Sites
Components
  • DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*GP*TP*TP*T)-3')
  • DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*GP*TP*TP*TP*AP*AP*AP*CP*TP*TP*TP*CP*CP*AP*GP*C)-3')
  • DNA (5'-D(P*AP*AP*AP*CP*TP*TP*TP*CP*CP*AP*GP*C)-3')
KeywordsDNA / minor groove / diamidine / single G / DNA recognition / small molecule
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsTerrell, J.R. / Ogbonna, E.N. / Paul, A. / 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: To be published
Title: Sequence Recognition in the Minor Groove: Single G Targeting by Diamidine Small Molecules
Authors: Terrell, J.R. / Ogbonna, E.N. / Paul, A. / Poon, G.M.K. / Wilson, W.D.
History
DepositionJul 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*GP*TP*TP*T)-3')
C: DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*GP*TP*TP*TP*AP*AP*AP*CP*TP*TP*TP*CP*CP*AP*GP*C)-3')
B: DNA (5'-D(P*AP*AP*AP*CP*TP*TP*TP*CP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,16523
Polymers14,6933
Non-polymers1,47220
Water2,846158
1
A: DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*GP*TP*TP*T)-3')
B: DNA (5'-D(P*AP*AP*AP*CP*TP*TP*TP*CP*CP*AP*GP*C)-3')
hetero molecules

A: DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*GP*TP*TP*T)-3')
B: DNA (5'-D(P*AP*AP*AP*CP*TP*TP*TP*CP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,28028
Polymers14,6484
Non-polymers1,63324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
2
C: DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*GP*TP*TP*TP*AP*AP*AP*CP*TP*TP*TP*CP*CP*AP*GP*C)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)16,04918
Polymers14,7382
Non-polymers1,31216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)39.173, 39.173, 479.389
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-103-

CA

21A-104-

CA

31C-104-

CA

41C-105-

CA

51C-229-

HOH

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Components

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DNA chain , 3 types, 3 molecules ACB

#1: DNA chain DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*GP*TP*TP*T)-3')


Mass: 3717.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*CP*TP*GP*GP*AP*AP*AP*GP*TP*TP*TP*AP*AP*AP*CP*TP*TP*TP*CP*CP*AP*GP*C)-3')


Mass: 7368.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*AP*AP*CP*TP*TP*TP*CP*CP*AP*GP*C)-3')


Mass: 3606.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 178 molecules

#4: Chemical ChemComp-A1AAQ / 4,4'-[pyridine-2,6-diylbis(methyleneoxy)]di(benzene-1-carboximidamide)


Mass: 375.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.62
Details: 0.8mM stock DNA solution in 7.5 mM HEPES, pH=6.6 buffer mixed 1:1 with well solution containing 10 mM HEPES, pH=8.6, 600 mM CaCl2, 42% PEG200

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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: 0.920071 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 29, 2022
RadiationMonochromator: Vertical DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920071 Å / Relative weight: 1
ReflectionResolution: 1.64→26.77 Å / Num. obs: 18393 / % possible obs: 99.15 % / Redundancy: 9.6 % / Biso Wilson estimate: 25.96 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.05469 / Rpim(I) all: 0.0196 / Rrim(I) all: 0.05824 / Net I/σ(I): 20.71
Reflection shellResolution: 1.64→1.699 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.2757 / Mean I/σ(I) obs: 4.76 / Num. unique obs: 1819 / CC1/2: 0.998 / CC star: 1 / Rpim(I) all: 0.09472 / Rrim(I) all: 0.2918 / % possible all: 97.49

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→26.77 Å / SU ML: 0.1694 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1024
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2672 1824 9.98 %
Rwork0.2198 16444 -
obs0.2245 18268 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.22 Å2
Refinement stepCycle: LAST / Resolution: 1.64→26.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 978 74 158 1210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01881155
X-RAY DIFFRACTIONf_angle_d2.00331764
X-RAY DIFFRACTIONf_chiral_restr0.1577190
X-RAY DIFFRACTIONf_plane_restr0.017358
X-RAY DIFFRACTIONf_dihedral_angle_d32.0341521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.25111340.23721193X-RAY DIFFRACTION97.07
1.68-1.730.33731330.23061206X-RAY DIFFRACTION97.59
1.73-1.790.26431370.23551263X-RAY DIFFRACTION98.38
1.79-1.850.25371360.22661217X-RAY DIFFRACTION99.19
1.85-1.930.23231380.21191234X-RAY DIFFRACTION99.56
1.93-2.020.31961390.22791256X-RAY DIFFRACTION99.79
2.02-2.120.32561390.2491254X-RAY DIFFRACTION99.86
2.12-2.250.29161400.23891258X-RAY DIFFRACTION99.86
2.26-2.430.28551430.23541283X-RAY DIFFRACTION100
2.43-2.670.24491390.24491259X-RAY DIFFRACTION100
2.67-3.060.2711450.24741302X-RAY DIFFRACTION99.79
3.06-3.850.2811430.20591300X-RAY DIFFRACTION98.5
3.85-26.770.24211580.1991419X-RAY DIFFRACTION99.62
Refinement TLS params.Method: refined / Origin x: 8.11661152259 Å / Origin y: 12.9946869074 Å / Origin z: 30.309023546 Å
111213212223313233
T0.196478296392 Å20.0127870636297 Å20.0013286192314 Å2-0.256045668259 Å20.0130952232242 Å2--0.190633908353 Å2
L0.0455078291971 °20.00381773744747 °2-0.470796491343 °2-0.0548866980726 °2-0.0154270910041 °2--5.77411440071 °2
S0.126581032735 Å °0.0107777890325 Å °-0.00421427509476 Å °0.0123343255824 Å °0.0910354949855 Å °0.000364585195734 Å °0.047259773034 Å °-0.294114546566 Å °-0.218217375093 Å °
Refinement TLS groupSelection details: all

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