HEADER RNA 10-MAR-05 1Z30 TITLE NMR STRUCTURE OF THE APICAL PART OF STEMLOOP D FROM CLOVERLEAF 1 OF TITLE 2 BOVINE ENTEROVIRUS 1 RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*CP*GP*UP*UP*CP*GP*UP*UP*AP*GP*AP*AP*CP*GP*UP*C) COMPND 3 -3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE SEQUENCE OF THIS RNA NATURALLY EXIST IN BOVINE SOURCE 4 ENTEROVIRUS 1 (VIRUS) KEYWDS CGUUAG RNA TETRALOOP, CUNCGG-TYPE BACKBONE CONFORMATION, A-FORM KEYWDS 2 HELIX, RNA EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR Y.IHLE,O.OHLENSCHLAGER,E.DUCHARDT,R.RAMACHANDRAN,M.GORLACH REVDAT 4 29-MAY-24 1Z30 1 REMARK REVDAT 3 02-MAR-22 1Z30 1 REMARK REVDAT 2 24-FEB-09 1Z30 1 VERSN REVDAT 1 26-APR-05 1Z30 0 JRNL AUTH Y.IHLE,O.OHLENSCHLAGER,S.HAFNER,E.DUCHARDT,M.ZACHARIAS, JRNL AUTH 2 S.SEITZ,R.ZELL,R.RAMACHANDRAN,M.GORLACH JRNL TITL A NOVEL CGUUAG TETRALOOP STRUCTURE WITH A CONSERVED JRNL TITL 2 YYNMGG-TYPE BACKBONE CONFORMATION FROM CLOVERLEAF 1 OF JRNL TITL 3 BOVINE ENTEROVIRUS 1 RNA JRNL REF NUCLEIC ACIDS RES. V. 33 2003 2005 JRNL REFN ISSN 0305-1048 JRNL PMID 15814817 JRNL DOI 10.1093/NAR/GKI501 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, REV. C, OPAL 2.6 REMARK 3 AUTHORS : VARIAN INC. (VNMR), LUGINBUHL (OPAL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 518 UPPER LIMIT DISTANCE CONSTRAINTS REMARK 3 DERIVED FROM NOE CROSS PEAKS, 184 TORSION ANGLE CONSTRAINTS REMARK 3 DEFINING 156 TORSION ANGLES, 36 HYDROGEN BOND CONSTRAINTS REMARK 4 REMARK 4 1Z30 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032233. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 283 REMARK 210 PH : 6.2; 6.2 REMARK 210 IONIC STRENGTH : 10MM KH2PO4/K2HPO4, 40MM KCL, REMARK 210 0.2MM EDTA; 10MM KH2PO4/K2HPO4, REMARK 210 40MM KCL, 0.2MM EDTA REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0MM U-[15N]-BEVSLDAP RNA; REMARK 210 0.9MM U-[13C,15N]-BEVSLDAP RNA; REMARK 210 0.9MM U-[13C,15N]-BEVSLDAP RNA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL 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 : VNMR 6.1, REV. C, XEASY 1.3.9, REMARK 210 CYANA 1.0.6, FOUND IMPLEMENTED REMARK 210 IN CYANA-1.0.6 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, ENERGY MINIMISATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY, TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 5 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 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 3 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 U A 6 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 A A 11 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 A A 11 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 A A 11 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 C A 15 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 U A 17 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 U A 17 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 5 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 5 A A 11 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 C A 15 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 6 A A 11 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 6 C A 15 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 7 U A 5 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 7 U A 6 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 8 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 8 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 8 A A 11 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 8 U A 17 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 9 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 9 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 9 U A 6 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 9 A A 11 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 10 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 10 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 10 A A 11 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 10 U A 17 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 11 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 11 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 11 U A 6 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 11 A A 11 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 11 U A 17 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 12 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 12 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 12 A A 11 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 12 C A 15 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 12 U A 17 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 13 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 13 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 13 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 13 A A 11 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 58 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 A A 11 0.10 SIDE CHAIN REMARK 500 1 G A 12 0.05 SIDE CHAIN REMARK 500 1 G A 16 0.07 SIDE CHAIN REMARK 500 2 G A 4 0.07 SIDE CHAIN REMARK 500 2 G A 8 0.06 SIDE CHAIN REMARK 500 2 A A 11 0.09 SIDE CHAIN REMARK 500 2 G A 16 0.07 SIDE CHAIN REMARK 500 3 G A 4 0.07 SIDE CHAIN REMARK 500 3 G A 8 0.06 SIDE CHAIN REMARK 500 3 A A 11 0.06 SIDE CHAIN REMARK 500 3 G A 16 0.07 SIDE CHAIN REMARK 500 4 G A 8 0.07 SIDE CHAIN REMARK 500 5 G A 8 0.07 SIDE CHAIN REMARK 500 5 A A 11 0.06 SIDE CHAIN REMARK 500 5 G A 16 0.08 SIDE CHAIN REMARK 500 6 G A 4 0.07 SIDE CHAIN REMARK 500 6 U A 5 0.06 SIDE CHAIN REMARK 500 6 A A 11 0.09 SIDE CHAIN REMARK 500 6 G A 12 0.06 SIDE CHAIN REMARK 500 6 G A 16 0.08 SIDE CHAIN REMARK 500 7 G A 8 0.06 SIDE CHAIN REMARK 500 7 A A 11 0.08 SIDE CHAIN REMARK 500 7 G A 12 0.06 SIDE CHAIN REMARK 500 7 G A 16 0.06 SIDE CHAIN REMARK 500 8 G A 8 0.06 SIDE CHAIN REMARK 500 8 A A 11 0.08 SIDE CHAIN REMARK 500 9 G A 8 0.06 SIDE CHAIN REMARK 500 9 A A 11 0.09 SIDE CHAIN REMARK 500 9 G A 16 0.08 SIDE CHAIN REMARK 500 10 G A 8 0.05 SIDE CHAIN REMARK 500 11 G A 12 0.07 SIDE CHAIN REMARK 500 12 G A 4 0.06 SIDE CHAIN REMARK 500 12 A A 11 0.07 SIDE CHAIN REMARK 500 12 G A 12 0.07 SIDE CHAIN REMARK 500 12 G A 16 0.07 SIDE CHAIN REMARK 500 13 A A 11 0.08 SIDE CHAIN REMARK 500 13 G A 16 0.06 SIDE CHAIN REMARK 500 14 G A 4 0.06 SIDE CHAIN REMARK 500 14 A A 11 0.08 SIDE CHAIN REMARK 500 14 G A 12 0.06 SIDE CHAIN REMARK 500 15 G A 8 0.07 SIDE CHAIN REMARK 500 15 G A 12 0.07 SIDE CHAIN REMARK 500 15 G A 16 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1Z30 A 1 18 PDB 1Z30 1Z30 1 18 SEQRES 1 A 18 G G C G U U C G U U A G A SEQRES 2 A 18 A C 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 MODEL 1