HEADER RNA 13-MAY-10 2KY0 TITLE THE STRUCTURE OF RNA INTERNAL LOOPS WITH TANDEM AG PAIRS: TITLE 2 5'GAGC/3'CGAG COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS TANDEM AG PAIRS, THERMODYNAMICS, IMINO AG PAIR, DUAL SYN GG PAIR, KEYWDS 2 EXTRAHELICAL U, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR N.B.HAMMOND,S.D.KENNEDY,D.H.TURNER REVDAT 2 21-JUL-10 2KY0 1 JRNL REVDAT 1 02-JUN-10 2KY0 0 JRNL AUTH N.B.HAMMOND,B.S.TOLBERT,R.KIERZEK,D.H.TURNER,S.D.KENNEDY JRNL TITL RNA INTERNAL LOOPS WITH TANDEM AG PAIRS: THE STRUCTURE OF JRNL TITL 2 THE 5'GAGU/3'UGAG LOOP CAN BE DRAMATICALLY DIFFERENT FROM JRNL TITL 3 OTHERS, INCLUDING 5'AAGU/3'UGAA. JRNL REF BIOCHEMISTRY V. 49 5817 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20481618 JRNL DOI 10.1021/BI100332R REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KY0 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAY-10. REMARK 100 THE RCSB ID CODE IS RCSB101714. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273; 288 REMARK 210 PH : 6.1; 6.1 REMARK 210 IONIC STRENGTH : 0.1; 0.1 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM RNA (5'-R(*GP*AP*CP*GP*AP* REMARK 210 GP*CP*GP*UP*CP*A)-3')-1, 80 MM SODIUM CHLORIDE-2, 10 MM SODIUM REMARK 210 PHOSPHATE-3, 0.5 MM EDTA-4, 90% H2O/10% D2O; 1 MM RNA (5'-R(*GP* REMARK 210 AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')-5, 80 MM SODIUM CHLORIDE-6, 10 REMARK 210 MM SODIUM PHOSPHATE-7, 0.5 MM EDTA-8, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 2D DQF-COSY; 2D REMARK 210 1H-31P HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.12, VNMR 6.1C, CNS 1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 A A 2 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 2 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 C A 3 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 5 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 C A 7 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 C A 10 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 A A 11 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 11 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 A B 13 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A B 13 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A B 13 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 C B 14 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 A B 16 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A B 16 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 C B 18 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 C B 21 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 A B 22 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A B 22 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 A A 2 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 A A 2 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 A A 2 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 C A 3 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 A A 5 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 C A 7 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 C A 10 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 A A 11 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 A A 11 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 11 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 A B 13 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 A B 13 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 C B 14 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 A B 16 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 A B 16 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 C B 18 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 C B 21 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 C B 21 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 A B 22 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 A B 22 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A B 22 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 3 A A 2 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 3 A A 2 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 A A 2 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 3 C A 3 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 3 A A 5 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 3 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 A A 5 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 3 C A 7 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 3 U A 9 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 224 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 G A 8 0.07 SIDE CHAIN REMARK 500 1 G B 19 0.07 SIDE CHAIN REMARK 500 2 G A 8 0.07 SIDE CHAIN REMARK 500 2 G B 19 0.07 SIDE CHAIN REMARK 500 3 G B 19 0.08 SIDE CHAIN REMARK 500 5 G A 8 0.07 SIDE CHAIN REMARK 500 6 G A 8 0.07 SIDE CHAIN REMARK 500 7 G A 8 0.07 SIDE CHAIN REMARK 500 9 G A 8 0.06 SIDE CHAIN REMARK 500 10 A A 11 0.06 SIDE CHAIN REMARK 500 10 G B 19 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KXZ RELATED DB: PDB REMARK 900 RELATED ID: 2KY1 RELATED DB: PDB REMARK 900 RELATED ID: 2KY2 RELATED DB: PDB REMARK 900 RELATED ID: 16950 RELATED DB: BMRB REMARK 900 RELATED ID: 16951 RELATED DB: BMRB REMARK 900 RELATED ID: 16952 RELATED DB: BMRB REMARK 900 RELATED ID: 16953 RELATED DB: BMRB DBREF 2KY0 A 1 11 PDB 2KY0 2KY0 1 11 DBREF 2KY0 B 12 22 PDB 2KY0 2KY0 12 22 SEQRES 1 A 11 G A C G A G C G U C A SEQRES 1 B 11 G A C G A G C G U C A 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 157 0 0 0 0 0 0 6 0 0 0 2 END