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- PDB-8f94: Structure of an alternating AT 16-mer: 5'-GCTGGATATATCCAGC-3 -

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Basic information

Entry
Database: PDB / ID: 8f94
TitleStructure of an alternating AT 16-mer: 5'-GCTGGATATATCCAGC-3
ComponentsDNA 16-mer
KeywordsDNA / AT sequence / Minor groove
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesDNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 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 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 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

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Assembly

Deposited unit
A: DNA 16-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,25910
Polymers4,8981
Non-polymers3619
Water1,69394
1
A: DNA 16-mer
hetero molecules

A: DNA 16-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,51820
Polymers9,7962
Non-polymers72118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_435x-y-2/3,-y-4/3,-z+2/31
Buried area1420 Å2
ΔGint-9 kcal/mol
Surface area5950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.769, 38.769, 159.771
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

41A-104-

CA

51A-231-

HOH

61A-265-

HOH

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Components

#1: DNA chain DNA 16-mer


Mass: 4898.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 47.85 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 1 mM DNA duplex 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: 1.08→26.63 Å / Num. obs: 20060 / % possible obs: 98.5 % / Redundancy: 2 % / Biso Wilson estimate: 15.5 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.01722 / Rpim(I) all: 0.01722 / Rrim(I) all: 0.02436 / Net I/σ(I): 22.55
Reflection shellResolution: 1.08→1.119 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1479 / Mean I/σ(I) obs: 6.48 / Num. unique obs: 1882 / CC1/2: 0.939 / CC star: 0.984 / Rpim(I) all: 0.1479 / Rrim(I) all: 0.2092 / % possible all: 92.88

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.08→26.63 Å / SU ML: 0.1107 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.7555
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2247 1996 9.98 %
Rwork0.2012 18004 -
obs0.2035 20000 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.64 Å2
Refinement stepCycle: LAST / Resolution: 1.08→26.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 325 9 94 428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0204364
X-RAY DIFFRACTIONf_angle_d2.0651560
X-RAY DIFFRACTIONf_chiral_restr0.118863
X-RAY DIFFRACTIONf_plane_restr0.034216
X-RAY DIFFRACTIONf_dihedral_angle_d33.2802156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.110.28551340.25221204X-RAY DIFFRACTION92.92
1.11-1.140.23291350.21771209X-RAY DIFFRACTION93.59
1.14-1.170.22391370.18921245X-RAY DIFFRACTION95.97
1.17-1.210.21241380.19191245X-RAY DIFFRACTION96.85
1.21-1.250.22751400.19151264X-RAY DIFFRACTION97.98
1.25-1.30.1851410.16841265X-RAY DIFFRACTION98.67
1.3-1.360.20761390.1611275X-RAY DIFFRACTION98.61
1.36-1.430.18961450.16121306X-RAY DIFFRACTION99.04
1.43-1.520.21961440.16161298X-RAY DIFFRACTION99.24
1.52-1.640.19011430.16191290X-RAY DIFFRACTION99.17
1.64-1.80.18721460.14691311X-RAY DIFFRACTION98.85
1.8-2.070.20771470.17241328X-RAY DIFFRACTION99.86
2.07-2.60.21131500.21541349X-RAY DIFFRACTION100
2.6-26.630.25321570.23221415X-RAY DIFFRACTION99.31

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