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

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Basic information

Entry
Database: PDB / ID: 9ckm
TitleThe 24mer DNA Duplex 5'-GCTGGAAAGTTTAAACTTTCCAGC-3' Bound by the Diamidine DB2457 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: 1.68 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. / Farahat, A.A. / Poon, G.M.K. / Wilson, W.D.
History
DepositionJul 9, 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)16,47527
Polymers14,6933
Non-polymers1,78324
Water2,990166
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)16,83138
Polymers14,6484
Non-polymers2,18434
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)16,12016
Polymers14,7382
Non-polymers1,38214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)39.280, 39.280, 480.772
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-101-

CA

21A-102-

CA

31A-103-

CA

41C-102-

CA

51C-103-

CA

61C-104-

CA

71C-105-

CA

81C-214-

HOH

91B-252-

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, 190 molecules

#4: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1AY9 / 4-{5-[5-(4-carbamimidoylphenyl)-1-methyl-1H-1,3-benzimidazol-2-yl]thiophen-2-yl}benzene-1-carboximidamide


Mass: 450.558 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H22N6S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
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: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2023
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.68→33.93 Å / Num. obs: 17320 / % possible obs: 99.72 % / Redundancy: 14.1 % / Biso Wilson estimate: 20.68 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06656 / Rpim(I) all: 0.01839 / Rrim(I) all: 0.06912 / Net I/σ(I): 24.52
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.6849 / Mean I/σ(I) obs: 3.63 / Num. unique obs: 1676 / CC1/2: 0.972 / CC star: 0.993 / Rpim(I) all: 0.1864 / Rrim(I) all: 0.7103 / % possible all: 99.34

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→33.93 Å / SU ML: 0.1948 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.2076
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2557 1726 9.99 %
Rwork0.2128 15557 -
obs0.217 17283 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.46 Å2
Refinement stepCycle: LAST / Resolution: 1.68→33.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 978 88 166 1232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01821169
X-RAY DIFFRACTIONf_angle_d2.01931792
X-RAY DIFFRACTIONf_chiral_restr0.09190
X-RAY DIFFRACTIONf_plane_restr0.019462
X-RAY DIFFRACTIONf_dihedral_angle_d31.9149529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.730.26951410.21661273X-RAY DIFFRACTION99.44
1.73-1.790.27631410.2241274X-RAY DIFFRACTION99.58
1.79-1.850.26471360.22031228X-RAY DIFFRACTION99.49
1.85-1.920.23921420.20151278X-RAY DIFFRACTION99.86
1.92-2.010.2561410.19411262X-RAY DIFFRACTION100
2.01-2.120.30341430.21211288X-RAY DIFFRACTION100
2.12-2.250.25461420.21871280X-RAY DIFFRACTION100
2.25-2.420.251430.21991282X-RAY DIFFRACTION100
2.42-2.670.28931450.22041304X-RAY DIFFRACTION100
2.67-3.050.29061450.23721316X-RAY DIFFRACTION99.93
3.05-3.840.27111460.19831322X-RAY DIFFRACTION98.72
3.85-33.930.21381610.20981450X-RAY DIFFRACTION99.94
Refinement TLS params.Method: refined / Origin x: 7.70547456382 Å / Origin y: 12.9602636345 Å / Origin z: 32.67078664 Å
111213212223313233
T0.251421100966 Å20.000686130933545 Å2-0.00711935779221 Å2-0.300889063752 Å20.0226177309511 Å2--0.207541917079 Å2
L-0.0458378562453 °2-0.0429975762824 °2-0.434648015829 °2--0.0291789568675 °20.0565927313114 °2--3.60537841043 °2
S0.0922323725163 Å °0.151263881921 Å °0.0229444080046 Å °-0.120881879502 Å °0.0582508692142 Å °-6.74874093754E-5 Å °0.0289496676102 Å °-0.428974916924 Å °-0.120261828603 Å °
Refinement TLS groupSelection details: all

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