HEADER RNA 25-OCT-05 2ES5 TITLE STRUCTURE OF THE SRE RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 R(*GP*GP*AP*GP*AP*GP*GP*CP*UP*CP*UP*GP*GP*CP*AP*GP*CP*UP*UP COMPND 4 *UP*UP*CP*C)-3'; COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: SRE RNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION KEYWDS RNA STRUCTURE, STEM-LOOP, PENTALOOP EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.H.T.ALLAIN REVDAT 3 24-FEB-09 2ES5 1 VERSN REVDAT 2 30-OCT-07 2ES5 1 JRNL REVDAT 1 24-JAN-06 2ES5 0 JRNL AUTH F.C.OBERSTRASS,A.LEE,R.STEFL,M.JANIS,G.CHANFREAU, JRNL AUTH 2 F.H.ALLAIN JRNL TITL SHAPE-SPECIFIC RECOGNITION IN THE STRUCTURE OF THE JRNL TITL 2 VTS1P SAM DOMAIN WITH RNA. JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 160 2006 JRNL REFN ISSN 1545-9993 JRNL PMID 16429156 JRNL DOI 10.1038/NSMB1038 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7.0 REMARK 3 AUTHORS : CASE, DA REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ES5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-05. REMARK 100 THE RCSB ID CODE IS RCSB035025. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50MM NACL, 50MM PHOSPHATE- REMARK 210 BUFFER REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 1MM RNA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ, 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE, DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, SPARKY, AMBER 7.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 G A 2 C5' - C4' - O4' ANGL. DEV. = 10.3 DEGREES REMARK 500 1 A A 3 C5' - C4' - O4' ANGL. DEV. = 10.4 DEGREES REMARK 500 1 G A 4 C5' - C4' - O4' ANGL. DEV. = 7.1 DEGREES REMARK 500 1 A A 5 C5' - C4' - O4' ANGL. DEV. = 8.1 DEGREES REMARK 500 1 G A 6 C5' - C4' - O4' ANGL. DEV. = 8.9 DEGREES REMARK 500 1 G A 6 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 G A 7 C5' - C4' - O4' ANGL. DEV. = 8.5 DEGREES REMARK 500 1 C A 8 C5' - C4' - O4' ANGL. DEV. = 9.5 DEGREES REMARK 500 1 C A 10 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 G A 12 C5' - C4' - O4' ANGL. DEV. = 5.5 DEGREES REMARK 500 1 G A 13 O4' - C1' - N9 ANGL. DEV. = -9.7 DEGREES REMARK 500 1 A A 15 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 C A 17 C5' - C4' - O4' ANGL. DEV. = 8.1 DEGREES REMARK 500 1 U A 18 C5' - C4' - O4' ANGL. DEV. = 9.8 DEGREES REMARK 500 1 U A 19 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 U A 20 C5' - C4' - O4' ANGL. DEV. = 8.8 DEGREES REMARK 500 1 U A 20 C4' - C3' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 U A 21 C5' - C4' - O4' ANGL. DEV. = 10.1 DEGREES REMARK 500 1 C A 22 C5' - C4' - O4' ANGL. DEV. = 9.3 DEGREES REMARK 500 1 C A 23 C5' - C4' - O4' ANGL. DEV. = 9.1 DEGREES REMARK 500 1 C A 23 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 G A 1 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 G A 2 C5' - C4' - O4' ANGL. DEV. = 8.2 DEGREES REMARK 500 2 G A 2 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 A A 3 C5' - C4' - O4' ANGL. DEV. = 8.4 DEGREES REMARK 500 2 A A 3 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 G A 4 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 A A 5 C5' - C4' - O4' ANGL. DEV. = 6.3 DEGREES REMARK 500 2 G A 6 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 C A 8 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 C A 10 O4' - C1' - N1 ANGL. DEV. = 7.8 DEGREES REMARK 500 2 G A 13 O4' - C1' - N9 ANGL. DEV. = -6.4 DEGREES REMARK 500 2 G A 13 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 G A 13 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 A A 15 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 2 A A 15 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 G A 16 C5' - C4' - O4' ANGL. DEV. = 5.4 DEGREES REMARK 500 2 G A 16 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 2 G A 16 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 C A 17 C5' - C4' - O4' ANGL. DEV. = 7.2 DEGREES REMARK 500 2 C A 17 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 C A 17 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 C A 17 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 U A 18 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 U A 18 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 U A 19 O4' - C1' - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 2 U A 20 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 U A 21 C5' - C4' - O4' ANGL. DEV. = 5.4 DEGREES REMARK 500 2 U A 21 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 C A 22 C5' - C4' - O4' ANGL. DEV. = 6.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 623 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 A A 15 0.06 SIDE_CHAIN REMARK 500 2 G A 4 0.09 SIDE_CHAIN REMARK 500 2 A A 5 0.06 SIDE_CHAIN REMARK 500 2 G A 6 0.08 SIDE_CHAIN REMARK 500 2 G A 7 0.07 SIDE_CHAIN REMARK 500 2 C A 8 0.07 SIDE_CHAIN REMARK 500 2 G A 13 0.07 SIDE_CHAIN REMARK 500 2 C A 17 0.08 SIDE_CHAIN REMARK 500 2 U A 19 0.07 SIDE_CHAIN REMARK 500 3 G A 2 0.07 SIDE_CHAIN REMARK 500 3 A A 3 0.06 SIDE_CHAIN REMARK 500 3 G A 4 0.09 SIDE_CHAIN REMARK 500 3 A A 5 0.06 SIDE_CHAIN REMARK 500 3 G A 6 0.08 SIDE_CHAIN REMARK 500 3 G A 7 0.08 SIDE_CHAIN REMARK 500 3 C A 8 0.08 SIDE_CHAIN REMARK 500 3 G A 13 0.08 SIDE_CHAIN REMARK 500 3 A A 15 0.06 SIDE_CHAIN REMARK 500 3 G A 16 0.09 SIDE_CHAIN REMARK 500 3 C A 17 0.08 SIDE_CHAIN REMARK 500 4 G A 2 0.07 SIDE_CHAIN REMARK 500 4 G A 4 0.10 SIDE_CHAIN REMARK 500 4 A A 5 0.07 SIDE_CHAIN REMARK 500 4 G A 6 0.09 SIDE_CHAIN REMARK 500 4 G A 7 0.08 SIDE_CHAIN REMARK 500 4 C A 8 0.08 SIDE_CHAIN REMARK 500 4 U A 9 0.08 SIDE_CHAIN REMARK 500 4 C A 10 0.08 SIDE_CHAIN REMARK 500 4 A A 15 0.06 SIDE_CHAIN REMARK 500 4 C A 17 0.09 SIDE_CHAIN REMARK 500 5 G A 2 0.06 SIDE_CHAIN REMARK 500 5 A A 3 0.06 SIDE_CHAIN REMARK 500 5 G A 4 0.07 SIDE_CHAIN REMARK 500 5 A A 5 0.06 SIDE_CHAIN REMARK 500 5 G A 6 0.09 SIDE_CHAIN REMARK 500 5 G A 7 0.10 SIDE_CHAIN REMARK 500 5 C A 8 0.10 SIDE_CHAIN REMARK 500 5 G A 13 0.10 SIDE_CHAIN REMARK 500 5 A A 15 0.08 SIDE_CHAIN REMARK 500 5 G A 16 0.07 SIDE_CHAIN REMARK 500 5 C A 17 0.09 SIDE_CHAIN REMARK 500 5 U A 18 0.07 SIDE_CHAIN REMARK 500 5 U A 19 0.08 SIDE_CHAIN REMARK 500 6 G A 2 0.06 SIDE_CHAIN REMARK 500 6 G A 4 0.08 SIDE_CHAIN REMARK 500 6 A A 5 0.06 SIDE_CHAIN REMARK 500 6 G A 6 0.07 SIDE_CHAIN REMARK 500 6 G A 7 0.08 SIDE_CHAIN REMARK 500 6 C A 8 0.07 SIDE_CHAIN REMARK 500 6 G A 13 0.09 SIDE_CHAIN REMARK 500 6 G A 16 0.08 SIDE_CHAIN REMARK 500 6 C A 17 0.07 SIDE_CHAIN REMARK 500 7 G A 2 0.07 SIDE_CHAIN REMARK 500 7 G A 6 0.07 SIDE_CHAIN REMARK 500 7 G A 7 0.08 SIDE_CHAIN REMARK 500 7 U A 11 0.15 SIDE_CHAIN REMARK 500 7 G A 13 0.08 SIDE_CHAIN REMARK 500 8 G A 2 0.07 SIDE_CHAIN REMARK 500 8 G A 6 0.10 SIDE_CHAIN REMARK 500 8 G A 7 0.07 SIDE_CHAIN REMARK 500 8 C A 8 0.08 SIDE_CHAIN REMARK 500 8 G A 13 0.11 SIDE_CHAIN REMARK 500 8 A A 15 0.08 SIDE_CHAIN REMARK 500 8 G A 16 0.08 SIDE_CHAIN REMARK 500 8 C A 17 0.08 SIDE_CHAIN REMARK 500 8 U A 20 0.07 SIDE_CHAIN REMARK 500 9 G A 2 0.07 SIDE_CHAIN REMARK 500 9 A A 5 0.07 SIDE_CHAIN REMARK 500 9 G A 6 0.10 SIDE_CHAIN REMARK 500 9 C A 8 0.08 SIDE_CHAIN REMARK 500 9 U A 11 0.14 SIDE_CHAIN REMARK 500 9 G A 13 0.12 SIDE_CHAIN REMARK 500 9 A A 15 0.05 SIDE_CHAIN REMARK 500 9 C A 17 0.07 SIDE_CHAIN REMARK 500 10 G A 4 0.09 SIDE_CHAIN REMARK 500 10 A A 5 0.07 SIDE_CHAIN REMARK 500 10 G A 6 0.09 SIDE_CHAIN REMARK 500 10 G A 7 0.09 SIDE_CHAIN REMARK 500 10 C A 8 0.09 SIDE_CHAIN REMARK 500 10 U A 9 0.10 SIDE_CHAIN REMARK 500 10 U A 11 0.12 SIDE_CHAIN REMARK 500 10 G A 16 0.07 SIDE_CHAIN REMARK 500 10 C A 17 0.10 SIDE_CHAIN REMARK 500 10 U A 18 0.07 SIDE_CHAIN REMARK 500 10 U A 19 0.08 SIDE_CHAIN REMARK 500 11 G A 2 0.07 SIDE_CHAIN REMARK 500 11 G A 4 0.08 SIDE_CHAIN REMARK 500 11 G A 6 0.09 SIDE_CHAIN REMARK 500 11 G A 7 0.07 SIDE_CHAIN REMARK 500 11 C A 8 0.08 SIDE_CHAIN REMARK 500 11 U A 9 0.07 SIDE_CHAIN REMARK 500 11 G A 13 0.10 SIDE_CHAIN REMARK 500 11 A A 15 0.07 SIDE_CHAIN REMARK 500 11 G A 16 0.07 SIDE_CHAIN REMARK 500 11 C A 17 0.09 SIDE_CHAIN REMARK 500 12 G A 2 0.07 SIDE_CHAIN REMARK 500 12 A A 3 0.06 SIDE_CHAIN REMARK 500 12 G A 7 0.08 SIDE_CHAIN REMARK 500 12 C A 8 0.07 SIDE_CHAIN REMARK 500 12 G A 13 0.09 SIDE_CHAIN REMARK 500 12 A A 15 0.06 SIDE_CHAIN REMARK 500 12 C A 17 0.08 SIDE_CHAIN REMARK 500 13 G A 2 0.07 SIDE_CHAIN REMARK 500 13 G A 6 0.09 SIDE_CHAIN REMARK 500 13 G A 7 0.08 SIDE_CHAIN REMARK 500 13 C A 8 0.08 SIDE_CHAIN REMARK 500 13 G A 13 0.09 SIDE_CHAIN REMARK 500 13 A A 15 0.06 SIDE_CHAIN REMARK 500 13 G A 16 0.07 SIDE_CHAIN REMARK 500 13 C A 17 0.07 SIDE_CHAIN REMARK 500 14 G A 2 0.07 SIDE_CHAIN REMARK 500 14 G A 4 0.08 SIDE_CHAIN REMARK 500 14 G A 6 0.11 SIDE_CHAIN REMARK 500 14 G A 7 0.10 SIDE_CHAIN REMARK 500 14 C A 8 0.10 SIDE_CHAIN REMARK 500 14 U A 9 0.06 SIDE_CHAIN REMARK 500 14 C A 10 0.10 SIDE_CHAIN REMARK 500 14 G A 13 0.07 SIDE_CHAIN REMARK 500 14 C A 17 0.09 SIDE_CHAIN REMARK 500 15 G A 4 0.07 SIDE_CHAIN REMARK 500 15 A A 5 0.07 SIDE_CHAIN REMARK 500 15 G A 6 0.09 SIDE_CHAIN REMARK 500 15 G A 7 0.09 SIDE_CHAIN REMARK 500 15 C A 8 0.10 SIDE_CHAIN REMARK 500 15 G A 13 0.10 SIDE_CHAIN REMARK 500 15 A A 15 0.07 SIDE_CHAIN REMARK 500 15 G A 16 0.10 SIDE_CHAIN REMARK 500 15 C A 17 0.09 SIDE_CHAIN REMARK 500 16 G A 2 0.07 SIDE_CHAIN REMARK 500 16 A A 3 0.06 SIDE_CHAIN REMARK 500 16 G A 4 0.08 SIDE_CHAIN REMARK 500 16 G A 7 0.06 SIDE_CHAIN REMARK 500 16 C A 8 0.08 SIDE_CHAIN REMARK 500 16 U A 9 0.06 SIDE_CHAIN REMARK 500 16 U A 11 0.14 SIDE_CHAIN REMARK 500 16 G A 13 0.09 SIDE_CHAIN REMARK 500 16 G A 16 0.07 SIDE_CHAIN REMARK 500 16 C A 17 0.09 SIDE_CHAIN REMARK 500 17 G A 2 0.06 SIDE_CHAIN REMARK 500 17 C A 8 0.08 SIDE_CHAIN REMARK 500 17 U A 9 0.08 SIDE_CHAIN REMARK 500 17 C A 10 0.07 SIDE_CHAIN REMARK 500 17 C A 17 0.07 SIDE_CHAIN REMARK 500 18 G A 7 0.06 SIDE_CHAIN REMARK 500 18 C A 8 0.06 SIDE_CHAIN REMARK 500 18 U A 9 0.08 SIDE_CHAIN REMARK 500 19 G A 2 0.07 SIDE_CHAIN REMARK 500 19 G A 4 0.08 SIDE_CHAIN REMARK 500 19 G A 6 0.08 SIDE_CHAIN REMARK 500 19 G A 7 0.07 SIDE_CHAIN REMARK 500 19 C A 8 0.08 SIDE_CHAIN REMARK 500 19 G A 13 0.09 SIDE_CHAIN REMARK 500 19 A A 15 0.08 SIDE_CHAIN REMARK 500 19 G A 16 0.08 SIDE_CHAIN REMARK 500 19 C A 17 0.08 SIDE_CHAIN REMARK 500 20 G A 4 0.08 SIDE_CHAIN REMARK 500 20 A A 5 0.06 SIDE_CHAIN REMARK 500 20 G A 6 0.11 SIDE_CHAIN REMARK 500 20 G A 7 0.09 SIDE_CHAIN REMARK 500 20 C A 8 0.08 SIDE_CHAIN REMARK 500 20 G A 13 0.12 SIDE_CHAIN REMARK 500 20 C A 17 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2ES5 A 1 23 PDB 2ES5 2ES5 1 23 SEQRES 1 A 23 G G A G A G G C U C U G G SEQRES 2 A 23 C A G C U U U 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 294 0 0 0 0 0 0 6 0 0 0 2 END