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- PDB-8fb4: Structure of an alternating AT 16-mer bound by diamidine DB1476: ... -

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Basic information

Entry
Database: PDB / ID: 8fb4
TitleStructure of an alternating AT 16-mer bound by diamidine DB1476: 5'-GCTGGATATATCCAGC-3
ComponentsDNA (5'-D(*GP*CP*TP*GP*GP*AP*TP*AP*TP*AP*TP*CP*CP*AP*GP*C)-3')
KeywordsDNA / AT sequence / Minor groove
Function / homologyChem-WFB / DNA / DNA (> 10)
Function and homology information
Biological speciesDNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsTerrell, J.R. / Ogbonna, 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
DepositionNov 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
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

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


Theoretical massNumber of molelcules
Total (without water)16,00520
Polymers14,6953
Non-polymers1,31017
Water2,684149
1
A: DNA (5'-D(*GP*CP*TP*GP*GP*AP*TP*AP*TP*AP*TP*CP*CP*AP*GP*C)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)11,14620
Polymers9,7962
Non-polymers1,35018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
2
B: DNA (5'-D(*GP*CP*TP*GP*GP*AP*TP*AP*TP*AP*TP*CP*CP*AP*GP*C)-3')
C: DNA (5'-D(*GP*CP*TP*GP*GP*AP*TP*AP*TP*AP*TP*CP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,43110
Polymers9,7962
Non-polymers6358
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.730, 38.730, 160.394
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-101-

WFB

21A-224-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 2 through 17)
d_2ens_1chain "B"
d_3ens_1(chain "C" and resid 2 through 17)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-ID
d_11ens_1DGDCA
d_21ens_1DGDCC
d_31ens_1DGDCD

NCS oper:
IDCodeMatrixVector
1given(0.999347244868, -0.00502407818672, 0.0357748908187), (-0.00504387235875, -0.999987172378, 0.000463067952279), (0.0357721054223, -0.000643209665234, -0.999359766428)0.0463000013206, -21.8340822375, 0.168247710237
2given(-0.483794905795, 0.874362824341, -0.0378436327231), (-0.874976919398, -0.484164153126, -0.000680697849893), (-0.0189177072831, 0.0327829870267, 0.999283441328)0.0143947218917, -21.7797955559, 0.21426608768

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Components

#1: DNA chain DNA (5'-D(*GP*CP*TP*GP*GP*AP*TP*AP*TP*AP*TP*CP*CP*AP*GP*C)-3')


Mass: 4898.191 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#2: Chemical ChemComp-WFB / 4,4'-(1H-benzimidazole-2,6-diyl)di(benzene-1-carboximidamide)


Mass: 354.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H18N6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 1 mM DNA duplex with 3 mM DB1976 annealed in 7.5 mM HEPES, pH=6.6 mixed at a 1:1 ratio with well solution containing 10 mM HEPES, pH=8.6, 600 mM CaCl2, 38% PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2022
RadiationMonochromator: Horizontal double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.49→28.41 Å / Num. obs: 23742 / % possible obs: 99.21 % / Redundancy: 2 % / Biso Wilson estimate: 20.63 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01058 / Rpim(I) all: 0.01058 / Rrim(I) all: 0.01497 / Net I/σ(I): 24.7
Reflection shellResolution: 1.49→1.544 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1428 / Mean I/σ(I) obs: 5.06 / Num. unique obs: 2299 / CC1/2: 0.966 / CC star: 0.991 / Rpim(I) all: 0.1428 / Rrim(I) all: 0.202 / % possible all: 99.01

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→28.41 Å / SU ML: 0.231 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7409
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2947 1998 8.45 %
Rwork0.2579 21649 -
obs0.2609 23647 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.75 Å2
Refinement stepCycle: LAST / Resolution: 1.49→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 975 69 149 1193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151152
X-RAY DIFFRACTIONf_angle_d1.5311766
X-RAY DIFFRACTIONf_chiral_restr0.0739189
X-RAY DIFFRACTIONf_plane_restr0.015558
X-RAY DIFFRACTIONf_dihedral_angle_d31.7776520
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.168844542952
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.140322955725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.530.39861380.35871502X-RAY DIFFRACTION98.97
1.53-1.570.37231350.30641488X-RAY DIFFRACTION99.27
1.57-1.610.30441340.26981543X-RAY DIFFRACTION99.05
1.62-1.670.29431400.23971475X-RAY DIFFRACTION97.94
1.67-1.730.2671390.24641499X-RAY DIFFRACTION98.14
1.73-1.80.23251410.22211523X-RAY DIFFRACTION98.75
1.8-1.880.29691420.25041520X-RAY DIFFRACTION99.58
1.88-1.980.31631490.24781555X-RAY DIFFRACTION99.71
1.98-2.10.30021420.25811543X-RAY DIFFRACTION99.94
2.1-2.260.26411390.25541561X-RAY DIFFRACTION100
2.26-2.490.26681470.27511549X-RAY DIFFRACTION100
2.49-2.850.3281460.24771590X-RAY DIFFRACTION99.94
2.85-3.590.28131470.25241592X-RAY DIFFRACTION98.81
3.59-28.410.30061590.26261709X-RAY DIFFRACTION99.26

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