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Open data
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Basic information
Entry | Database: PDB / ID: 1hlx | ||||||||||||||||||
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Title | P1 HELIX NUCLEIC ACIDS (DNA/RNA) RIBONUCLEIC ACID | ||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / DOUBLE HELIX / GROUP I / SELF-SPLICING INTRON / UUCG TETRALOOP HAIRPIN / WOBBLE PAIR | Function / homology | RNA / RNA (> 10) | ![]() Method | SOLUTION NMR | ![]() Allain, F.H.-T. / Varani, G. | ![]() ![]() Title: Structure of the P1 helix from group I self-splicing introns. Authors: Allain, F.H. / Varani, G. #1: ![]() Title: Divalent Metal Ion Binding to a Conserved Wobble Pair Defining the Upstream Site of Cleavage of Group I Self-Splicing Introns Authors: Allain, F.H.-T. / Varani, G. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 247.5 KB | Display | ![]() |
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PDB format | ![]() | 207.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 320.3 KB | Display | ![]() |
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Full document | ![]() | 427.2 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 13.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: RNA chain | Mass: 6376.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: IN VITRO TRANSCRIPTION / ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: THE RNA SAMPLE WAS OBTAINED BY IN VITRO TRANSCRIPTION USING THE T7 RNA POLYMERASE AND A DOUBLE STRANDED DNA TEMPLATE. THE RNA WAS THEN PURIFIED BY GEL ELECTROPHORESIS. |
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Sample preparation
Crystal grow | *PLUS Method: other / Details: NMR |
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Processing
Software |
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NMR software | Name: ![]() | ||||||||||||
Refinement | Software ordinal: 1 Details: NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 637 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 X-PLOR STANDARD BOND LENGTHS AND ANGLES. ...Details: NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 637 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 X-PLOR STANDARD BOND LENGTHS AND ANGLES. ANGLES IN THE SUGAR RING WERE MODIFIED ACCORDING TO THE VALUES FOUND IN "PRINCIPLE OF NUCLEIC ACID STRUCTURE" BY SAENGER. STARTING WITH 30 STRUCTURES WITH RANDOMIZED BACKBONE TORSION ANGLES, 20 STRUCTURES WERE FOUND TO HAVE CONVERGED AFTER A PERIOD OF SIMULATED ANNEALING WITH ONLY NOE-DERIVED (581) AND H-BOND CONSTRAINTS (20) FOLLOWED BY A PERIOD OF REFINEMENT WHERE 100 DIHEDRAL CONSTRAINTS DERIVED FROM J COUPLING ANALYSIS AND PHOSPHORUS CHEMICAL SHIFT VALUE WERE ADDED. NO DIHEDRAL ANGLE VIOLATIONS AND 0-2 NOE VIOLATIONS BETWEEN 0.1 - 0.3 ANGSTROMS WERE FOUND IN EACH OF THE 20 CONVERGED STRUCTURES. | ||||||||||||
NMR constraints | NOE constraints total: 581 / Hydrogen bond constraints total count: 20 | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 30 / Conformers submitted total number: 20 |