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Yorodumi- PDB-4jrd: Crystal structure of the parallel double-stranded helix of poly(A) RNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jrd | ||||||||||||||||||
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Title | Crystal structure of the parallel double-stranded helix of poly(A) RNA | ||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / PARALLEL DOUBLE HELIX / POLY(A) / MRNA / PABP / Poly(A) motif | Function / homology | AMMONIUM ION / RNA / RNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1 Å | Authors | Safaee, N. / Noronha, A.M. / Kozlov, G. / Rodionov, D. / Wilds, C.J. / Sheldrick, G.M. / Gehring, K. | Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2013 | Title: Structure of the parallel duplex of poly(A) RNA: evaluation of a 50 year-old prediction. Authors: Safaee, N. / Noronha, A.M. / Rodionov, D. / Kozlov, G. / Wilds, C.J. / Sheldrick, G.M. / Gehring, K. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jrd.cif.gz | 35.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jrd.ent.gz | 27.2 KB | Display | PDB format |
PDBx/mmJSON format | 4jrd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jrd_validation.pdf.gz | 419 KB | Display | wwPDB validaton report |
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Full document | 4jrd_full_validation.pdf.gz | 419.5 KB | Display | |
Data in XML | 4jrd_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 4jrd_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/4jrd ftp://data.pdbj.org/pub/pdb/validation_reports/jr/4jrd | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 3576.306 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-NH4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 1.49 Å3/Da / Density % sol: 17.29 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: RNA WATER SOLUTION PLUS BUFFER (10 MM HEPES, 50 MM NACL, 0.5 MM TCEP, PH 7.0) MIXED 1:1 V/V WITH 2 M (NH4)2SO4 + 0.2 M NH4NO3 AND EQUILIBRATED AGAINST 2 M (NH4)2SO4 + 0.2 M NH4NO3, VAPOR ...Details: RNA WATER SOLUTION PLUS BUFFER (10 MM HEPES, 50 MM NACL, 0.5 MM TCEP, PH 7.0) MIXED 1:1 V/V WITH 2 M (NH4)2SO4 + 0.2 M NH4NO3 AND EQUILIBRATED AGAINST 2 M (NH4)2SO4 + 0.2 M NH4NO3, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1→41 Å / Num. all: 23042 / Num. obs: 22972 / % possible obs: 92.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): -3 / Redundancy: 2.73 % / Rmerge(I) obs: 0.0944 / Net I/σ(I): 34.35 | ||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1→1.1 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.1419 / Mean I/σ(I) obs: 4.72 / % possible all: 73.1 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1→41 Å / Num. parameters: 5165 / Num. restraintsaints: 6773 / Cross valid method: FREE R / σ(F): 1
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Solvent computation | Solvent model: BABINET | |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 242 / Occupancy sum non hydrogen: 571 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→41 Å
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Refine LS restraints |
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