HEADER RNA 03-JUL-07 2JSE TITLE NMR REVEALS ABSENCE OF HYDROGEN BONDING IN ADJACENT UU AND AG TITLE 2 MISMATCHES IN AN ISOLATED INTERNAL LOOP FROM RIBOSOMAL RNA. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*GP*GP*AP*GP*UP*GP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*AP*UP*CP*UP*CP*C)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: T7 POLYMERASE USED TO TRANSCRIBE THE RNA FROM A SOURCE 4 SYNTHETIC DUPLEX DNA TEMPLATE KEYWDS NMR STRUCTURE OF RNA LOOP 5' GUGG 3' / 3' CUAC 5', G BASE FLIPPED KEYWDS 2 OUT, 2X2 THERMODYNAMICS, LACK OF HYDROGEN BONDING, ABSENCE OF KEYWDS 3 HYDROGEN BONDING, UU INTERNAL LOOP, UU/AG INTERNAL LOOP, AG INTERNAL KEYWDS 4 LOOP, INTERNAL LOOP FROM PROTEIN L11 BINDING SITE, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR N.SHANKAR REVDAT 3 16-MAR-22 2JSE 1 REMARK REVDAT 2 24-FEB-09 2JSE 1 VERSN REVDAT 1 20-NOV-07 2JSE 0 JRNL AUTH N.SHANKAR,T.XIA,S.D.KENNEDY,T.R.KRUGH,D.H.MATHEWS,D.H.TURNER JRNL TITL NMR REVEALS THE ABSENCE OF HYDROGEN BONDING IN ADJACENT UU JRNL TITL 2 AND AG MISMATCHES IN AN ISOLATED INTERNAL LOOP FROM JRNL TITL 3 RIBOSOMAL RNA JRNL REF BIOCHEMISTRY V. 46 12665 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17929882 JRNL DOI 10.1021/BI700802S REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS, CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JSE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000100230. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 80 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.5 MM RNA, 90% H2O/10% D2O; 0.6 REMARK 210 MM C13, N15 RNA, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRDRAW, SPARKY, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY AND LEAST DISTANCE AND REMARK 210 ANGLE VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 DBREF 2JSE A 1 22 PDB 2JSE 2JSE 1 22 SEQRES 1 A 22 G G A G U G G C C G A A A SEQRES 2 A 22 G G C A U C U C C CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1