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Yorodumi- PDB-1yzd: Crystal structure of an RNA duplex containing a site specific 2'-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yzd | ||||||||||||||||||
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Title | Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair | ||||||||||||||||||
Components | RNA 5'-R(*Keywords | RNA / 2'-AMINE / DUPLEX | Function / homology | RNA / RNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | Authors | Gherghe, C.M. / Krahn, J.M. / Weeks, K.M. | Citation | Journal: J.Am.Chem.Soc. / Year: 2005 | Title: Crystal structures, reactivity and inferred acylation transition States for 2'-amine substituted RNA. Authors: Gherghe, C.M. / Krahn, J.M. / Weeks, K.M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yzd.cif.gz | 37.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yzd.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 1yzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yzd_validation.pdf.gz | 402.8 KB | Display | wwPDB validaton report |
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Full document | 1yzd_full_validation.pdf.gz | 403.6 KB | Display | |
Data in XML | 1yzd_validation.xml.gz | 4 KB | Display | |
Data in CIF | 1yzd_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/1yzd ftp://data.pdbj.org/pub/pdb/validation_reports/yz/1yzd | HTTPS FTP |
-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 on special symmetry positions |
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-Components
#1: RNA chain | Mass: 5097.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: chemically synthesized #2: Chemical | ChemComp-CA / | #3: 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: 2.11 Å3/Da / Density % sol: 41.76 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 8 Details: MPD, sodium cacodylate, spermidine, magnesium chloride, calcium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 24, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→31.7 Å / Num. all: 7277 / Num. obs: 6646 / % possible obs: 91.4 % / Observed criterion σ(I): 1 / Redundancy: 21.79 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.06 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.18→2.28 Å / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.37 / Num. unique all: 405 / Rsym value: 0.37 / % possible all: 57.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→8.07 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 852998.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.0361 Å2 / ksol: 0.405429 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→8.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.49 Å / Rfactor Rfree error: 0.067 / Total num. of bins used: 6
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Xplor file |
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