+Open data
-Basic information
Entry | Database: PDB / ID: 8fdp | ||||||||||||||||||||||||||||
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Title | The native structure of a dodecamer: 5'-CGCAAATTTGCG-3 | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / AT sequence / Minor groove | Function / homology | DNA / DNA (> 10) | Function and homology information Biological species | Homo sapiens (human) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | Authors | Ogbonna, E. / Wilson, W.D. | Funding support | United States, 1items |
Citation | Journal: 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. #1: Journal: J Mol Biol / Year: 1992 Title: Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG)2. An examination of propeller twist and minor-groove water structure at 2.2 A resolution. Authors: Edwards, K.J. / Brown, D.G. / Spink, N. / Skelly, J.V. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fdp.cif.gz | 28.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fdp.ent.gz | 14.7 KB | Display | PDB format |
PDBx/mmJSON format | 8fdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fdp_validation.pdf.gz | 366.6 KB | Display | wwPDB validaton report |
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Full document | 8fdp_full_validation.pdf.gz | 366.5 KB | Display | |
Data in XML | 8fdp_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 8fdp_validation.cif.gz | 3.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/8fdp ftp://data.pdbj.org/pub/pdb/validation_reports/fd/8fdp | HTTPS FTP |
-Related structure data
Related structure data | 8ec1C 8ed6C 8edaC 8edbC 8f1sC 8f1vC 8f20C 8f2wC 8f2yC 8f94C 8fb4C 8fdqC 8fdrC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (0.769370461347, -0.63625107547, -0.0570408815595), (-0.637091318857, -0.770776081865, 0.00434546447809), (-0.0467305536422, 0.0329969784512, -0.998362386496)Vector: 17. ...NCS oper: (Code: given Matrix: (0.769370461347, -0.63625107547, -0.0570408815595), Vector: |
-Components
#1: DNA chain | Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: CGCAAATTTGCG is a self-complementary DNA. Chain B: 5'-CGCAAATTTGCG-3' Chain C: 3'-GCGTTTAAACGC-5' Source: (synth.) Homo sapiens (human) #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.89 % |
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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: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→23.34 Å / Num. obs: 5921 / % possible obs: 99.5 % / Redundancy: 2 % / Biso Wilson estimate: 42.54 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01009 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.88→1.95 Å / Num. unique obs: 577 / CC1/2: 0.995 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→23.34 Å / SU ML: 0.2564 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.3418 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: 39.41 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→23.34 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.886903761 Å | |||||||||||||||||||||||||||||||||||
LS refinement shell |
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