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Yorodumi- PDB-249d: STRUCTURAL COMPARISON BETWEEN THE D(CTAG) SEQUENCE IN OLIGONUCLEO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 249d | ||||||||||||||||||
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Title | STRUCTURAL COMPARISON BETWEEN THE D(CTAG) SEQUENCE IN OLIGONUCLEOTIDES AND TRP AND MET REPRESSOR-OPERATOR COMPLEXES | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | Authors | Urpi, L. / Tereshko, V. / Malinina, L. / Huynh-Dinh, T. / Subirana, J.A. | Citation | Journal: Nat.Struct.Biol. / Year: 1996 Title: Structural comparison between the d(CTAG) sequence in oligonucleotides and trp and met repressor-operator complexes. Authors: Urpi, L. / Tereshko, V. / Malinina, L. / Huynh-Dinh, T. / Subirana, J.A. #1: Journal: Biochemistry / Year: 1996 Title: Structure of the B-DNA Oligomers d(CGCTAGCG) and d(CGCTCTAGAGCG) in New Crystal Forms Authors: Tereshko, R.V. / Urpi, L. / Malinina, L. / Huynh-Dinh, T. / Subirana, J.A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 249d.cif.gz | 41.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb249d.ent.gz | 28.5 KB | Display | PDB format |
PDBx/mmJSON format | 249d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/49/249d ftp://data.pdbj.org/pub/pdb/validation_reports/49/249d | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: Chemical | ChemComp-CA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.91 % | ||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION | ||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Detector | Type: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER / Date: Apr 3, 1989 |
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Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.25 Å / Num. obs: 5276 / % possible obs: 88.9 % / Rmerge(I) obs: 0.09 |
Reflection | *PLUS Highest resolution: 2.25 Å / % possible obs: 88.9 % / Rmerge(I) obs: 0.09 |
-Processing
Software |
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Refinement | Resolution: 2.25→8 Å / σ(F): 2
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.25→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |