HEADER RNA 18-FEB-13 2M58 TITLE STRUCTURE OF 2'-5' AG1 LARIAT FORMING RIBOZYME IN ITS INACTIVE STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (59-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RNA, LARIAT, 2'-5' BRANCHING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR T.CARLOMAGNO,I.AMATA,L.CODUTTI,M.FALB,J.FOHRER,B.SIMON REVDAT 3 15-MAY-24 2M58 1 REMARK REVDAT 2 14-JUN-23 2M58 1 REMARK LINK REVDAT 1 03-APR-13 2M58 0 JRNL AUTH T.CARLOMAGNO,I.AMATA,L.CODUTTI,M.FALB,J.FOHRER,P.MASIEWICZ, JRNL AUTH 2 B.SIMON JRNL TITL STRUCTURAL PRINCIPLES OF RNA CATALYSIS IN A 2'-5' JRNL TITL 2 LARIAT-FORMING RIBOZYME. JRNL REF J.AM.CHEM.SOC. V. 135 4403 2013 JRNL REFN ISSN 0002-7863 JRNL PMID 23472843 JRNL DOI 10.1021/JA311868T REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX, ARIA REMARK 3 AUTHORS : ACCELRYS SOFTWARE INC. (FELIX), LINGE, O'DONOGHUE REMARK 3 AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WATER REFINED REMARK 4 REMARK 4 2M58 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000103224. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.6 REMARK 210 IONIC STRENGTH : 0.020 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 400 UM [U-100% 13C; U-100% 15N] REMARK 210 ADENOSINE-5'-MONOPHOSPHATE, 100% REMARK 210 D2O; 300 UM [U-100% 13C; U-100% REMARK 210 15N] GUANOSINE-5'-MONOPHOSPHATE, REMARK 210 300 UM [U-100% 13C; U-100% 15N] REMARK 210 GUANOSINE-5'-TRIPHOSPHATE, 100% REMARK 210 D2O; 500 UM [U-100% 13C; U-100% REMARK 210 15N] CYTIDINE-5'-MONOPHOSPHATE, REMARK 210 100% D2O; 300 UM [U-100% 13C; U- REMARK 210 100% 15N] URIDINE-5'- REMARK 210 MONOPHOSPHATE, 100% D2O; 500 UM REMARK 210 [U-100% 13C; U-100% 15N] REMARK 210 ADENOSINE-5'-MONOPHOSPHATE, 500 REMARK 210 UM [U-100% 13C; U-100% 15N] REMARK 210 URIDINE-5'-MONOPHOSPHATE, 100% REMARK 210 D2O; 500 UM [U-100% 13C; U-100% REMARK 210 15N] ADENOSINE-5'-MONOPHOSPHATE, REMARK 210 500 UM [U-100% 13C; U-100% 15N] REMARK 210 URIDINE-5'-MONOPHOSPHATE, 500 UM REMARK 210 [U-100% 13C; U-100% 15N] REMARK 210 GUANOSINE-5'-MONOPHOSPHATE, 500 REMARK 210 UM [U-100% 13C; U-100% 15N] REMARK 210 CYTIDINE-5'-MONOPHOSPHATE, 100% REMARK 210 D2O; 500 UM ADENOSINE-5'- REMARK 210 MONOPHOSPHATE, 500 UM URIDINE-5'- REMARK 210 MONOPHOSPHATE, 500 UM GUANOSINE- REMARK 210 5'-MONOPHOSPHATE, 500 UM REMARK 210 CYTIDINE-5'-MONOPHOSPHATE, 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 RIBOSE; 2D 1H-13C HSQC BASE; 2D REMARK 210 HNN-COSY; 2D IMINO NOESY; 3D REMARK 210 HSCNB/HBCNB; 3D HCCH-COSY-TOCSY; REMARK 210 3D 13C-EDITED/ 12C-FILTERED REMARK 210 NOESY; 3D 13C-EDITED/ 13C- REMARK 210 FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HO2' U A 13 O6 G A 16 1.50 REMARK 500 REMARK 500 REMARK: NULL 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 15 C3' - C2' - C1' ANGL. DEV. = -4.6 DEGREES REMARK 500 1 G A 16 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 A A 52 C1' - O4' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 2 C A 15 C3' - C2' - C1' ANGL. DEV. = -4.7 DEGREES REMARK 500 2 G A 16 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 C A 43 C1' - O4' - C4' ANGL. DEV. = -5.3 DEGREES REMARK 500 3 C A 15 C3' - C2' - C1' ANGL. DEV. = -4.5 DEGREES REMARK 500 3 G A 16 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 4 C A 15 C3' - C2' - C1' ANGL. DEV. = -4.3 DEGREES REMARK 500 4 G A 16 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 G A 16 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 6 C A 15 C3' - C2' - C1' ANGL. DEV. = -4.5 DEGREES REMARK 500 6 G A 16 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 7 G A 16 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 8 C A 15 C3' - C2' - C1' ANGL. DEV. = -4.5 DEGREES REMARK 500 8 G A 16 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 9 C A 15 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 9 G A 16 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 10 C A 15 C3' - C2' - C1' ANGL. DEV. = -4.5 DEGREES REMARK 500 10 G A 16 O4' - C1' - N9 ANGL. DEV. = 4.9 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 A A 8 0.05 SIDE CHAIN REMARK 500 1 G A 16 0.05 SIDE CHAIN REMARK 500 2 A A 8 0.05 SIDE CHAIN REMARK 500 2 C A 15 0.06 SIDE CHAIN REMARK 500 2 G A 16 0.06 SIDE CHAIN REMARK 500 2 G A 41 0.06 SIDE CHAIN REMARK 500 2 C A 45 0.06 SIDE CHAIN REMARK 500 3 A A 8 0.06 SIDE CHAIN REMARK 500 3 C A 15 0.07 SIDE CHAIN REMARK 500 3 G A 16 0.06 SIDE CHAIN REMARK 500 3 C A 47 0.06 SIDE CHAIN REMARK 500 3 U A 56 0.06 SIDE CHAIN REMARK 500 4 G A 16 0.05 SIDE CHAIN REMARK 500 5 C A 15 0.06 SIDE CHAIN REMARK 500 5 G A 16 0.06 SIDE CHAIN REMARK 500 5 C A 45 0.06 SIDE CHAIN REMARK 500 6 G A 16 0.05 SIDE CHAIN REMARK 500 6 C A 45 0.07 SIDE CHAIN REMARK 500 6 C A 47 0.06 SIDE CHAIN REMARK 500 7 G A 16 0.05 SIDE CHAIN REMARK 500 9 A A 8 0.06 SIDE CHAIN REMARK 500 9 C A 15 0.06 SIDE CHAIN REMARK 500 9 G A 16 0.06 SIDE CHAIN REMARK 500 9 C A 45 0.06 SIDE CHAIN REMARK 500 9 C A 47 0.07 SIDE CHAIN REMARK 500 10 A A 8 0.06 SIDE CHAIN REMARK 500 10 G A 16 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19040 RELATED DB: BMRB DBREF 2M58 A 1 59 PDB 2M58 2M58 1 59 SEQRES 1 A 59 GTP G A A G A A A G G G C U SEQRES 2 A 59 U C G G C C A C U C A A A SEQRES 3 A 59 C U A C A G A G A C G C C SEQRES 4 A 59 A G U C A C U C A G A U A SEQRES 5 A 59 U C C U G G U MODRES 2M58 GTP A 1 G GUANOSINE-5'-TRIPHOSPHATE HET GTP A 1 44 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE FORMUL 1 GTP C10 H16 N5 O14 P3 LINK O3' GTP A 1 P G A 2 1555 1555 1.61 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 HETATM 1 PG GTP A 1 13.414 -12.885 5.831 1.00 0.00 P HETATM 2 O1G GTP A 1 13.727 -13.634 7.071 1.00 0.00 O HETATM 3 O2G GTP A 1 14.750 -12.202 5.309 1.00 0.00 O HETATM 4 O3G GTP A 1 12.397 -11.804 5.870 1.00 0.00 O HETATM 5 O3B GTP A 1 12.996 -13.918 4.683 1.00 0.00 O HETATM 6 PB GTP A 1 14.238 -14.410 3.802 1.00 0.00 P HETATM 7 O1B GTP A 1 15.455 -14.370 4.653 1.00 0.00 O HETATM 8 O2B GTP A 1 14.243 -13.598 2.568 1.00 0.00 O HETATM 9 O3A GTP A 1 14.049 -15.972 3.505 1.00 0.00 O HETATM 10 PA GTP A 1 13.936 -16.425 1.972 1.00 0.00 P HETATM 11 O1A GTP A 1 12.704 -17.243 1.862 1.00 0.00 O HETATM 12 O2A GTP A 1 15.220 -17.097 1.651 1.00 0.00 O HETATM 13 O5' GTP A 1 13.769 -15.228 0.936 1.00 0.00 O HETATM 14 C5' GTP A 1 14.720 -15.024 -0.106 1.00 0.00 C HETATM 15 C4' GTP A 1 14.151 -14.116 -1.172 1.00 0.00 C HETATM 16 O4' GTP A 1 12.773 -13.794 -0.859 1.00 0.00 O HETATM 17 C3' GTP A 1 14.799 -12.747 -1.303 1.00 0.00 C HETATM 18 O3' GTP A 1 16.003 -12.806 -2.059 1.00 0.00 O HETATM 19 C2' GTP A 1 13.725 -11.945 -2.030 1.00 0.00 C HETATM 20 O2' GTP A 1 13.795 -12.130 -3.429 1.00 0.00 O HETATM 21 C1' GTP A 1 12.435 -12.577 -1.501 1.00 0.00 C HETATM 22 N9 GTP A 1 11.723 -11.723 -0.556 1.00 0.00 N HETATM 23 C8 GTP A 1 11.873 -11.679 0.808 1.00 0.00 C HETATM 24 N7 GTP A 1 11.121 -10.777 1.380 1.00 0.00 N HETATM 25 C5 GTP A 1 10.430 -10.190 0.328 1.00 0.00 C HETATM 26 C6 GTP A 1 9.466 -9.146 0.326 1.00 0.00 C HETATM 27 O6 GTP A 1 9.018 -8.511 1.292 1.00 0.00 O HETATM 28 N1 GTP A 1 9.017 -8.857 -0.960 1.00 0.00 N HETATM 29 C2 GTP A 1 9.448 -9.502 -2.098 1.00 0.00 C HETATM 30 N2 GTP A 1 8.897 -9.108 -3.253 1.00 0.00 N HETATM 31 N3 GTP A 1 10.344 -10.474 -2.110 1.00 0.00 N HETATM 32 C4 GTP A 1 10.790 -10.765 -0.871 1.00 0.00 C HETATM 33 H5' GTP A 1 14.981 -15.983 -0.557 1.00 0.00 H HETATM 34 H5'' GTP A 1 15.623 -14.572 0.302 1.00 0.00 H HETATM 35 H4' GTP A 1 14.272 -14.618 -2.132 1.00 0.00 H HETATM 36 H3' GTP A 1 15.061 -12.325 -0.334 1.00 0.00 H HETATM 37 H2' GTP A 1 13.789 -10.892 -1.749 1.00 0.00 H HETATM 38 HO2' GTP A 1 14.130 -11.306 -3.805 1.00 0.00 H HETATM 39 H1' GTP A 1 11.748 -12.825 -2.309 1.00 0.00 H HETATM 40 H8 GTP A 1 12.543 -12.328 1.352 1.00 0.00 H HETATM 41 HN1 GTP A 1 8.328 -8.119 -1.063 1.00 0.00 H HETATM 42 HN21 GTP A 1 9.167 -9.551 -4.124 1.00 0.00 H HETATM 43 HN22 GTP A 1 8.208 -8.366 -3.262 1.00 0.00 H HETATM 44 HO5' GTP A 1 15.339 -12.927 5.031 1.00 0.00 H