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Yorodumi- PDB-1lux: NMR SOLUTION STRUCTURE OF THE ANTICODON OF YEAST TRNA-PHE WITH 3 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lux | ||||||||||||||||||
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Title | NMR SOLUTION STRUCTURE OF THE ANTICODON OF YEAST TRNA-PHE WITH 3 MODIFICATIONS (OMC32 OMG34 M5C40) | ||||||||||||||||||
Components | 5'-R(*Keywords | RNA / TRNA / ANTICODON STEM LOOP / TRNA DOMAIN / RNA HAIRPIN / 2'-O-METHYL / M5C | Function / homology | RNA / RNA (> 10) | Function and homology information Method | SOLUTION NMR / global fold by distance geometry. refinement by simulated annealing using the amber forcefield | Authors | Stuart, J.W. / Koshlap, K.M. / Guenther, R.H. / Agris, P.F. | Citation | Journal: J.Mol.Biol. / Year: 2003 | Title: Naturally-occurring Modification Restricts the Anticodon Domain Conformational Space of tRNA(Phe). Authors: Stuart, J.W. / Koshlap, K.M. / Guenther, R. / Agris, P.F. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lux.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lux.ent.gz | 104.6 KB | Display | PDB format |
PDBx/mmJSON format | 1lux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lux_validation.pdf.gz | 338.8 KB | Display | wwPDB validaton report |
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Full document | 1lux_full_validation.pdf.gz | 399.3 KB | Display | |
Data in XML | 1lux_validation.xml.gz | 7 KB | Display | |
Data in CIF | 1lux_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/1lux ftp://data.pdbj.org/pub/pdb/validation_reports/lu/1lux | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 5508.404 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: SEQUENCE WITH NATURALLY OCCURRING MODIFICATIONS SYNTHESIZED USING PHOSPHORAMIDITE CHEMISTRY. |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques. |
-Sample preparation
Details | Contents: 1.6 mM RNA, 10 mM cacodylate buffer, pH 5.6, 0.1 mM EDTA |
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Sample conditions | pH: 5.6 / Pressure: 1 atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: global fold by distance geometry. refinement by simulated annealing using the amber forcefield Software ordinal: 1 Details: 271 restraints (258 NOE-Derived, 13 h-bond), 95 dihedral angle | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 10 |