HEADER RNA 14-DEC-07 2JYM TITLE SOLUTION STRUCTURE OF STEM-LOOP ALPHA OF THE HEPATITIS B TITLE 2 VIRUS POST-TRANSCRIPTIONAL REGULATORY ELEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*GP*GP*CP*UP*CP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*UP*GP*GP*AP COMPND 4 *GP*UP*C)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS HEPATITIS B VIRUS, POST-TRANSCRIPTIONAL REGULATORY ELEMENT, KEYWDS 2 STEM-LOOP ALPHA, NMR SOLUTION STRUCTURE, RNA EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR O.OHLENSCHLAGER,M.GORLACH,M.SCHWALBE REVDAT 2 24-FEB-09 2JYM 1 VERSN REVDAT 1 29-APR-08 2JYM 0 JRNL AUTH M.SCHWALBE,O.OHLENSCHLAGER,A.MARCHANKA, JRNL AUTH 2 R.RAMACHANDRAN,S.HAFNER,T.HEISE,M.GORLACH JRNL TITL SOLUTION STRUCTURE OF STEM-LOOP ALPHA OF THE JRNL TITL 2 HEPATITIS B VIRUS POST-TRANSCRIPTIONAL REGULATORY JRNL TITL 3 ELEMENT JRNL REF NUCLEIC ACIDS RES. V. 36 1681 2008 JRNL REFN ISSN 0305-1048 JRNL PMID 18263618 JRNL DOI 10.1093/NAR/GKN006 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPAL REMARK 3 AUTHORS : LUGINBUHL, GUNTERT, BILLETER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE CALCULATION, ENERGY REMARK 3 MINIMISATION REMARK 4 REMARK 4 2JYM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-DEC-07. REMARK 100 THE RCSB ID CODE IS RCSB100453. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 293 REMARK 210 PH : 6.2; 6.2 REMARK 210 IONIC STRENGTH : 50; 50 REMARK 210 PRESSURE : AMBIENT ATM; AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 1MM [U-100% 13C; U-100% 15N] REMARK 210 RNA, 10MM POTASSIUM PHOSPHATE, REMARK 210 40MM POTASSIUM CHLORIDE, 0. MM REMARK 210 EDTA, 90% H2O/10% D2O; 1MM [U- REMARK 210 100% 13C; U-100% 15N] RNA, REMARK 210 10MM POTASSIUM PHOSPHATE, 40MM REMARK 210 POTASSIUM CHLORIDE, 0.2MM REMARK 210 EDTA, 99% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC, 2D 1H-13C REMARK 210 HSQC, 2D 1H-1H NOESY, 3D 1H- REMARK 210 13C NOESY, 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.0, XEASY, VNMR, OPAL REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY REMARK 210 SIMULATED ANNEALING, FORCE REMARK 210 FIELD-BASED EM REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 C A 10 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 13 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 U A 16 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 G A 18 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 G A 13 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 C A 15 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 U A 16 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 G A 6 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 C A 10 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 G A 13 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 C A 15 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 U A 16 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 4 G A 13 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 4 U A 16 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 U A 21 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 5 C A 10 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 G A 13 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 5 U A 16 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 6 C A 10 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 G A 13 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 6 U A 16 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 7 G A 13 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 7 C A 15 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 7 U A 16 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 7 U A 21 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 8 G A 13 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 8 C A 15 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 8 U A 16 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 8 U A 21 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 9 C A 10 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 9 G A 13 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 9 U A 16 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 10 G A 13 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 10 U A 16 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 11 G A 13 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 11 C A 15 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 11 U A 16 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 12 G A 13 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 12 U A 16 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 13 G A 13 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 13 U A 16 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 13 U A 21 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 14 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 14 C A 10 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 14 G A 13 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 14 U A 16 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 15 C A 10 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 15 G A 13 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 15 U A 16 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES 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 2 0.06 SIDE_CHAIN REMARK 500 1 C A 7 0.07 SIDE_CHAIN REMARK 500 1 A A 8 0.08 SIDE_CHAIN REMARK 500 1 G A 9 0.08 SIDE_CHAIN REMARK 500 1 G A 13 0.08 SIDE_CHAIN REMARK 500 1 U A 16 0.07 SIDE_CHAIN REMARK 500 1 G A 17 0.05 SIDE_CHAIN REMARK 500 1 C A 22 0.07 SIDE_CHAIN REMARK 500 2 G A 2 0.07 SIDE_CHAIN REMARK 500 2 C A 7 0.06 SIDE_CHAIN REMARK 500 2 A A 8 0.08 SIDE_CHAIN REMARK 500 2 G A 9 0.08 SIDE_CHAIN REMARK 500 2 G A 12 0.07 SIDE_CHAIN REMARK 500 2 G A 13 0.06 SIDE_CHAIN REMARK 500 2 U A 16 0.09 SIDE_CHAIN REMARK 500 2 G A 17 0.05 SIDE_CHAIN REMARK 500 3 G A 2 0.08 SIDE_CHAIN REMARK 500 3 A A 8 0.06 SIDE_CHAIN REMARK 500 3 A A 11 0.06 SIDE_CHAIN REMARK 500 3 G A 13 0.05 SIDE_CHAIN REMARK 500 3 U A 16 0.07 SIDE_CHAIN REMARK 500 3 G A 17 0.07 SIDE_CHAIN REMARK 500 4 A A 8 0.10 SIDE_CHAIN REMARK 500 4 G A 9 0.08 SIDE_CHAIN REMARK 500 4 A A 11 0.08 SIDE_CHAIN REMARK 500 4 G A 12 0.08 SIDE_CHAIN REMARK 500 4 G A 13 0.06 SIDE_CHAIN REMARK 500 4 G A 17 0.06 SIDE_CHAIN REMARK 500 5 G A 2 0.06 SIDE_CHAIN REMARK 500 5 C A 7 0.07 SIDE_CHAIN REMARK 500 5 A A 8 0.07 SIDE_CHAIN REMARK 500 5 G A 13 0.07 SIDE_CHAIN REMARK 500 5 C A 22 0.06 SIDE_CHAIN REMARK 500 6 G A 2 0.06 SIDE_CHAIN REMARK 500 6 C A 7 0.08 SIDE_CHAIN REMARK 500 6 A A 8 0.08 SIDE_CHAIN REMARK 500 6 A A 11 0.07 SIDE_CHAIN REMARK 500 6 G A 13 0.08 SIDE_CHAIN REMARK 500 7 A A 8 0.08 SIDE_CHAIN REMARK 500 7 G A 13 0.08 SIDE_CHAIN REMARK 500 7 U A 16 0.06 SIDE_CHAIN REMARK 500 8 C A 7 0.07 SIDE_CHAIN REMARK 500 8 A A 8 0.09 SIDE_CHAIN REMARK 500 8 C A 10 0.06 SIDE_CHAIN REMARK 500 8 U A 16 0.07 SIDE_CHAIN REMARK 500 8 G A 17 0.05 SIDE_CHAIN REMARK 500 9 A A 8 0.06 SIDE_CHAIN REMARK 500 9 G A 9 0.07 SIDE_CHAIN REMARK 500 9 G A 12 0.06 SIDE_CHAIN REMARK 500 9 G A 13 0.05 SIDE_CHAIN REMARK 500 9 U A 16 0.10 SIDE_CHAIN REMARK 500 9 G A 17 0.07 SIDE_CHAIN REMARK 500 10 G A 2 0.07 SIDE_CHAIN REMARK 500 10 C A 7 0.08 SIDE_CHAIN REMARK 500 10 A A 8 0.08 SIDE_CHAIN REMARK 500 10 G A 9 0.07 SIDE_CHAIN REMARK 500 10 C A 15 0.07 SIDE_CHAIN REMARK 500 10 G A 17 0.05 SIDE_CHAIN REMARK 500 10 C A 22 0.07 SIDE_CHAIN REMARK 500 11 G A 2 0.06 SIDE_CHAIN REMARK 500 11 C A 7 0.08 SIDE_CHAIN REMARK 500 11 A A 8 0.06 SIDE_CHAIN REMARK 500 11 G A 9 0.07 SIDE_CHAIN REMARK 500 11 G A 12 0.07 SIDE_CHAIN REMARK 500 11 G A 13 0.06 SIDE_CHAIN REMARK 500 11 U A 16 0.07 SIDE_CHAIN REMARK 500 12 G A 12 0.07 SIDE_CHAIN REMARK 500 12 G A 13 0.06 SIDE_CHAIN REMARK 500 12 U A 16 0.08 SIDE_CHAIN REMARK 500 12 G A 17 0.06 SIDE_CHAIN REMARK 500 12 C A 22 0.07 SIDE_CHAIN REMARK 500 13 A A 8 0.08 SIDE_CHAIN REMARK 500 13 U A 16 0.08 SIDE_CHAIN REMARK 500 13 G A 17 0.06 SIDE_CHAIN REMARK 500 14 G A 12 0.07 SIDE_CHAIN REMARK 500 14 G A 13 0.06 SIDE_CHAIN REMARK 500 14 U A 16 0.09 SIDE_CHAIN REMARK 500 14 G A 17 0.07 SIDE_CHAIN REMARK 500 14 C A 22 0.06 SIDE_CHAIN REMARK 500 15 A A 8 0.05 SIDE_CHAIN REMARK 500 15 A A 11 0.06 SIDE_CHAIN REMARK 500 15 G A 13 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2JYM A 1 22 PDB 2JYM 2JYM 1 22 SEQRES 1 A 22 G G C U C G C A G C A G G SEQRES 2 A 22 U C U G G A G U 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 MASTER 221 0 0 0 0 0 0 6 0 0 0 2 END