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Open data
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Basic information
Entry | Database: PDB / ID: 8f2y | ||||||||||||||||||||||||||||
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Title | Structure of an alternating AT dodecamer: 5'-CGCGATATCGCG-3 | ||||||||||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / AT sequence / Minor groove | Function / homology | DNA / DNA (> 10) | ![]() Biological species | ![]() Method | ![]() ![]() ![]() ![]() Ogbonna, E.N. / Wilson, W.D. | Funding support | | ![]()
![]() ![]() 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. #1: ![]() Title: Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment. Authors: Coll, M. / Aymami, J. / van der Marel, G.A. / van Boom, J.H. / Rich, A. / Wang, A.H. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.3 KB | Display | ![]() |
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PDB format | ![]() | 21.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 771.2 KB | Display | ![]() |
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Full document | ![]() | 771.3 KB | Display | |
Data in XML | ![]() | 3.9 KB | Display | |
Data in CIF | ![]() | 5.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ec1C ![]() 8ed6C ![]() 8edaC ![]() 8edbC ![]() 8f1sC ![]() 8f1vC ![]() 8f20C ![]() 8f2wC ![]() 8f94C ![]() 8fb4C ![]() 8fdpC ![]() 8fdqC ![]() 8fdrC ![]() 1bnaS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (0.710580337659, -0.702920432949, -0.0312801642587), (-0.703505296372, -0.710554893073, -0.0138579185359), (-0.0124852596732, 0.0318529256598, -0.999414583353)Vector: 19. ...NCS oper: (Code: given Matrix: (0.710580337659, -0.702920432949, -0.0312801642587), Vector: |
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Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Native alternating AT DNA dodecamer (5'-CGCGATATCGCG-3'). Source: (synth.) ![]() #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, SODIUM CACODYLATE TRIHYDRATE, SPERMINE TETRACHLORIDE, SODIUM CHLROIDE, MAGNESIUM HEXAHYDRATE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→25.71 Å / Num. obs: 7017 / % possible obs: 99.6 % / Redundancy: 2 % / Biso Wilson estimate: 21.95 Å2 / CC1/2: 0.994 / CC star: 0.999 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.78→1.84 Å / Rmerge(I) obs: 0.1557 / Num. unique obs: 692 / CC1/2: 0.955 / Rpim(I) all: 0.1557 / Rrim(I) all: 0.2202 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BNA Resolution: 1.78→25.71 Å / SU ML: 0.2132 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.3698 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→25.71 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 2.05791582552 Å | ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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