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Yorodumi- PDB-2krl: The ensemble of the solution global structures of the 102-nt ribo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2krl | ||||||
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Title | The ensemble of the solution global structures of the 102-nt ribosome binding structure element of the turnip crinkle virus 3' UTR RNA | ||||||
Components | RNA (102-MER) | ||||||
Keywords | RNA / SAXS / 3' UTR / global structure of large RNAs | ||||||
Function / homology | : / RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||
Biological species | Turnip crinkle virus | ||||||
Method | SOLUTION NMR / SOLUTION SCATTERING / simulated annealing, duplex-orientation restrained | ||||||
Model details | closest to the average, model 1 | ||||||
Authors | Zuo, X. / Wang, J. / Yu, P. / Eyler, D. / Xu, H. / Starich, M. / Tiede, D. / Simon, A. / Kasprzak, W. / Schwieters, C. / Shapiro, B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus. Authors: Zuo, X. / Wang, J. / Yu, P. / Eyler, D. / Xu, H. / Starich, M.R. / Tiede, D.M. / Simon, A.E. / Kasprzak, W. / Schwieters, C.D. / Shapiro, B.A. / Wang, Y.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2krl.cif.gz | 628.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2krl.ent.gz | 533.8 KB | Display | PDB format |
PDBx/mmJSON format | 2krl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2krl_validation.pdf.gz | 328.9 KB | Display | wwPDB validaton report |
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Full document | 2krl_full_validation.pdf.gz | 519 KB | Display | |
Data in XML | 2krl_validation.xml.gz | 59.5 KB | Display | |
Data in CIF | 2krl_validation.cif.gz | 89.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/2krl ftp://data.pdbj.org/pub/pdb/validation_reports/kr/2krl | 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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NMR ensembles |
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-Components
#1: RNA chain | Mass: 32978.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Turnip crinkle virus / References: GenBank: M22445.2 |
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-Experimental details
-Experiment
Experiment |
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NMR experiment |
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NMR details | Text: MORE DETAILS ON STRUTURE DETERMINATION IN REMARK 265 |
-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 50 / pH: 6.8 / Pressure: ambient / Temperature: 298.2 K |
-Data collection
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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Soln scatter | Type: x-ray / Buffer name: 50 MM TRIS, 0.5 MM MgCl2 / Conc. range: 1.0-5.0 Data analysis software list: GNOM, HOME-WRITTEN SCRIPTS IN IGOR AND MATLAB Data reduction software list: MARDETECTOR, HOME-WRITTEN PROGRAM Detector specific: MARRESEARCH GMBH, GERMANY / Detector type: MARCCD 165 / Mean guiner radius: 30.9 nm / Mean guiner radius esd: 0.4 nm / Num. of time frames: 20 / Protein length: 110 / Sample pH: 6.8 / Source beamline: 12-ID,18-ID / Source class: Y / Source type: APS ARGONNE / Temperature: 298 K |
-Processing
NMR software |
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Refinement | Method: simulated annealing, duplex-orientation restrained / Software ordinal: 1 Details: the orientations of all duplexes were restrained during the SA calculation | ||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 | ||||||||||||
Soln scatter model | Method: SIMULATED ANNEALING METHOD WITH RESTRAINTS OF X-RAY SCATTERING DATA, RDC DATA, GENERIC A-FORM GEOMETRIC DISTANCE IN DUPLEXES, GENERIC A-FORM LIKE STACKING, NMR DETECTED HYDROGEN BONDS, AND ...Method: SIMULATED ANNEALING METHOD WITH RESTRAINTS OF X-RAY SCATTERING DATA, RDC DATA, GENERIC A-FORM GEOMETRIC DISTANCE IN DUPLEXES, GENERIC A-FORM LIKE STACKING, NMR DETECTED HYDROGEN BONDS, AND SAXS MOLECULAR ENVELOPE DIMENISIONAL MEASUREMENTS. Conformer selection criteria: STRUCTURES WITH LOWEST TOTAL ENERGY. THE TOTAL ENERGY INCLUDES PSEUDO-POTENTIALS OF SCATTERING TERM, RDC TERM, HYDROGEN BONDING TERM, AND OTHER REGULAR PSEUDO-POTENTIALS ...Conformer selection criteria: STRUCTURES WITH LOWEST TOTAL ENERGY. THE TOTAL ENERGY INCLUDES PSEUDO-POTENTIALS OF SCATTERING TERM, RDC TERM, HYDROGEN BONDING TERM, AND OTHER REGULAR PSEUDO-POTENTIALS IMPLEMENTED IN XPLOR-NIH. Details: SAXS MOLECULAR ENVELOPE WAS GENERATED USING AB INITIO MODEL CONSTRUCTION FROM SAXS BY DAMMIN AND DAMAVER. G2G WAS USED TO GENERATE INITIAL STRUCTURE. REFERENCE OF G2G IS : X. Zuo, J. Wang, P. ...Details: SAXS MOLECULAR ENVELOPE WAS GENERATED USING AB INITIO MODEL CONSTRUCTION FROM SAXS BY DAMMIN AND DAMAVER. G2G WAS USED TO GENERATE INITIAL STRUCTURE. REFERENCE OF G2G IS : X. Zuo, J. Wang, P. Yu, D. Eyler, H. Xu, M.R. Starich, D.M. Tiede, A.E. Simon, W. Kasprzak, C.D. Schwieters, B.A. Shapiro, Y.-X. WANG, A Method for Helical RNA Global Structure Determination in Solution Using Small-Angle X-Ray Scattering and NMR Measurements; JOURNAL OF MOLECULAR BIOLOGY 2009, 393(3), 717-734. Entry fitting list: G2G INITIAL STRUCTURE / Num. of conformers calculated: 100 / Num. of conformers submitted: 10 / Representative conformer: 1 Software list: G2G, DAMMIN AND DAMAVER IN ATSAS 2.1, XPLOR-NIH |