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Yorodumi- PDB-1i7j: CRYSTAL STRUCTURE OF 2'-O-ME(CGCGCG)2: AN RNA DUPLEX AT 1.19 A RE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i7j | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF 2'-O-ME(CGCGCG)2: AN RNA DUPLEX AT 1.19 A RESOLUTION. 2-METHYL-2,4-PENTANEDIOL AND MAGNESIUM BINDING. | ||||||||||||||||||
Components | 5'-R(*Keywords | RNA / 2'-O-MeRNA duplex / 2-methyl-2 / 4-pentanediol / magnesium / groove hydration and binding | Function / homology | RNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å | Authors | Adamiak, D.A. / Rypniewski, W.R. / Milecki, J. / Adamiak, R.W. | Citation | Journal: Nucleic Acids Res. / Year: 2001 Title: The 1.19 A X-ray structure of 2'-O-Me(CGCGCG)(2) duplex shows dehydrated RNA with 2-methyl-2,4-pentanediol in the minor groove. Authors: Adamiak, D.A. / Rypniewski, W.R. / Milecki, J. / Adamiak, R.W. #1: Journal: Nucleic Acids Res. / Year: 1997 Title: CRYSTAL STRUCTURE OF 2'-O-ME(CGCGCG)2: AN RNA DUPLEX AT 1.3 A RESOLUTION. HYDRATION PATTERN OF 2'-O-METHYLATED RNA Authors: Adamiak, D.A. / Milecki, J. / Popenda, W. / Adamiak, R.W. / Dauter, A. / Rypniewski, W.R. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i7j.cif.gz | 32.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i7j.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 1i7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i7j_validation.pdf.gz | 383.5 KB | Display | wwPDB validaton report |
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Full document | 1i7j_full_validation.pdf.gz | 390.1 KB | Display | |
Data in XML | 1i7j_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 1i7j_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/1i7j ftp://data.pdbj.org/pub/pdb/validation_reports/i7/1i7j | HTTPS FTP |
-Related structure data
Related structure data | 310dS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 1990.361 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / #3: Chemical | #4: 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: 1.73 Å3/Da / Density % sol: 38 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15 mM MgCl2, 1 mM spermine tetrahydrochloride and 30-40% 2-methyl-2,4-pentanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 3, 1996 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→20 Å / Num. obs: 8715 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.19→1.21 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / Num. unique all: 415 / % possible all: 94 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 8715 / Num. measured all: 150605 |
Reflection shell | *PLUS % possible obs: 94 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 310D Resolution: 1.19→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CCP4
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Refinement step | Cycle: LAST / Resolution: 1.19→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.19→1.21 Å /
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |