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Yorodumi- PDB-17ra: BRANCHPOINT HELIX FROM YEAST AND BINDING SITE FOR PHAGE GA/MS2 CO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 17ra | ||||||
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Title | BRANCHPOINT HELIX FROM YEAST AND BINDING SITE FOR PHAGE GA/MS2 COAT PROTEINS, NMR, 12 STRUCTURES | ||||||
Components | RNA | ||||||
Keywords | RNA / BRANCHPOINT HELIX / PHAGE MS2 / BULGE / BASE TRIPLE / RIBONUCLEIC ACID | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Nikonowicz, E.P. / Smith, J.S. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: NMR structure and dynamics of an RNA motif common to the spliceosome branch-point helix and the RNA-binding site for phage GA coat protein. Authors: Smith, J.S. / Nikonowicz, E.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 17ra.cif.gz | 161.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb17ra.ent.gz | 133.2 KB | Display | PDB format |
PDBx/mmJSON format | 17ra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 17ra_validation.pdf.gz | 325.2 KB | Display | wwPDB validaton report |
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Full document | 17ra_full_validation.pdf.gz | 395.4 KB | Display | |
Data in XML | 17ra_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 17ra_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/7r/17ra ftp://data.pdbj.org/pub/pdb/validation_reports/7r/17ra | 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: 6729.044 Da / Num. of mol.: 1 / Fragment: RBS AND START SITE FOR PHAGE GA REPLICASE GENE / Mutation: A5U, A6U / Source method: obtained synthetically Details: IN VITRO SYNTHESIS FROM DNA TEMPLATE USING T7 RNA POLYMERASE. HAIRPIN CORRESPONDS TO NT -16 - +5 OF PHAGE GA REPLICASE AND THE YEAST PRE-MRNA BRANCHPOINT HELIX |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: FURTHER DETAILS OF DATA ACQUISITION AND STRUCTURE CALCULATION CAN BE FOUND IN THE METHODS SECTION OF THE MANUSCRIPT LISTED ABOVE. MODELS 1-6 ARE MINIMIZED STRUCTURES CALCULATED WITHOUT BASE ...Text: FURTHER DETAILS OF DATA ACQUISITION AND STRUCTURE CALCULATION CAN BE FOUND IN THE METHODS SECTION OF THE MANUSCRIPT LISTED ABOVE. MODELS 1-6 ARE MINIMIZED STRUCTURES CALCULATED WITHOUT BASE PAIR CONSTRAINTS FOR A6, A7, AND U16. MODELS 7-12 ARE MINIMIZED STRUCTURES CALCULATED USING A6-U16 BASE PAIR CONSTRAINTS AND AN A7 N1H-U16 O2 HYDROGEN BOND. |
-Sample preparation
Details | Contents: 10% H2O/90% D2O, 100% D2O |
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Sample conditions | Ionic strength: 20 mM / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz |
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-Processing
Software |
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NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. | ||||||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 75 / Conformers submitted total number: 12 |