HEADER RNA 04-JAN-05 1YG4 TITLE SOLUTION STRUCTURE OF THE SCYLV P1-P2 FRAMESHIFTING TITLE 2 PSEUDOKNOT, REGULARIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCYLV RNA PSEUDOKNOT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: IN VITRO TRANSCRIPTION KEYWDS RNA PSEUDOKNOT; RIBOSOMAL FRAMESHIFTING; PROTONATED CYTIDINE EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR P.V.CORNISH,M.HENNIG,D.P.GIEDROC REVDAT 2 24-FEB-09 1YG4 1 VERSN REVDAT 1 13-DEC-05 1YG4 0 JRNL AUTH P.V.CORNISH,M.HENNIG,D.P.GIEDROC JRNL TITL A LOOP 2 CYTIDINE-STEM 1 MINOR GROOVE INTERACTION JRNL TITL 2 AS A POSITIVE DETERMINANT FOR JRNL TITL 3 PSEUDOKNOT-STIMULATED -1 RIBOSOMAL FRAMESHIFTING JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 12694 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 16123125 JRNL DOI 10.1073/PNAS.0506166102 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR-NIH 2.9.7 REMARK 3 AUTHORS : G.M. CLORE , J.KUSZEWSKI, C.D. SCHWIETERS, AND REMARK 3 N.TJANDRA REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YG4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-05. REMARK 100 THE RCSB ID CODE IS RCSB031474. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 298; 298 REMARK 210 PH : 6.0; 6.0; 6.0 REMARK 210 IONIC STRENGTH : 100MM KCL; 5MM MGCL2; 100MM REMARK 210 KCL; 5MM MGCL2; 100MM KCL; 5MM REMARK 210 MGCL2 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM SCYLV PSEUDOKNOT, 100MM REMARK 210 KCL, 5MM MGCL2, PH6.0; 2MM REMARK 210 SCYLV PSEUDOKNOT, 100MM KCL, REMARK 210 5MM MGCL2, PH6.0; 2MM SCYLV REMARK 210 PSEUDOKNOT, 100MM KCL, 5MM REMARK 210 MGCL2, PH6.0, 12.5MG/ML PF1 REMARK 210 PHAGE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 3D_13C-SEPARATED_ REMARK 210 NOESY, CT-TROSY AND CT- REMARK 210 ANTITROSY, J-MODULATED HSQC, REMARK 210 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ, 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA, AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN, BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 97.027.12.56, SPARKY REMARK 210 3.110, X-PLOR-NIH 2.9.7 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 25 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : AVERAGED STRUCTURE 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: 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 O2' A A 20 O5' A A 21 1.95 REMARK 500 O2' A A 21 O5' A A 22 2.12 REMARK 500 N2 G A 12 O4' C A 14 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 G A 6 C2' G A 6 C1' -0.050 REMARK 500 G A 7 N1 G A 7 C2 0.058 REMARK 500 G A 7 C6 G A 7 N1 -0.045 REMARK 500 C A 11 N3 C A 11 C4 -0.048 REMARK 500 G A 12 C5' G A 12 C4' 0.108 REMARK 500 C A 14 C2' C A 14 C1' -0.070 REMARK 500 C A 15 N1 C A 15 C6 0.040 REMARK 500 A A 16 C2' A A 16 C1' -0.078 REMARK 500 A A 16 C6 A A 16 N1 -0.046 REMARK 500 A A 16 N9 A A 16 C4 0.052 REMARK 500 U A 18 C2' U A 18 C1' -0.108 REMARK 500 A A 22 C6 A A 22 N1 -0.044 REMARK 500 C A 28 N1 C A 28 C6 0.063 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 A A 3 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 A A 3 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 A A 3 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 G A 4 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 G A 4 C5 - N7 - C8 ANGL. DEV. = -3.3 DEGREES REMARK 500 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 G A 4 N9 - C4 - C5 ANGL. DEV. = 2.9 DEGREES REMARK 500 G A 6 O4' - C1' - N9 ANGL. DEV. = 14.1 DEGREES REMARK 500 G A 6 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 G A 6 N9 - C4 - C5 ANGL. DEV. = -2.5 DEGREES REMARK 500 G A 7 P - O5' - C5' ANGL. DEV. = 9.9 DEGREES REMARK 500 G A 7 O4' - C1' - N9 ANGL. DEV. = 13.3 DEGREES REMARK 500 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 6 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES REMARK 500 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 G A 9 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 C A 11 P - O5' - C5' ANGL. DEV. = 14.3 DEGREES REMARK 500 G A 12 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 G A 12 C5 - N7 - C8 ANGL. DEV. = -3.0 DEGREES REMARK 500 G A 12 N7 - C8 - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 G A 12 C8 - N9 - C4 ANGL. DEV. = -4.4 DEGREES REMARK 500 A A 13 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 A A 16 O4' - C1' - N9 ANGL. DEV. = 10.8 DEGREES REMARK 500 A A 16 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 A A 16 N9 - C4 - C5 ANGL. DEV. = -3.6 DEGREES REMARK 500 C A 17 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 U A 18 C5' - C4' - O4' ANGL. DEV. = 5.9 DEGREES REMARK 500 U A 18 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 U A 19 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 A A 20 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 21 C3' - C2' - C1' ANGL. DEV. = 5.5 DEGREES REMARK 500 A A 21 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 A A 21 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 A A 20 C3' - O3' - P ANGL. DEV. = 12.1 DEGREES REMARK 500 A A 22 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 A A 23 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 A A 23 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 A A 24 C5' - C4' - O4' ANGL. DEV. = 6.0 DEGREES REMARK 500 A A 24 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 A A 24 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 A A 26 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 A A 26 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 C A 27 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 G A 29 N7 - C8 - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 G A 29 C8 - N9 - C4 ANGL. DEV. = -5.1 DEGREES REMARK 500 G A 29 N9 - C4 - C5 ANGL. DEV. = 2.7 DEGREES REMARK 500 G A 30 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 G A 30 C8 - N9 - C4 ANGL. DEV. = -3.7 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 A A 3 0.09 SIDE_CHAIN REMARK 500 G A 4 0.07 SIDE_CHAIN REMARK 500 U A 5 0.07 SIDE_CHAIN REMARK 500 G A 6 0.08 SIDE_CHAIN REMARK 500 G A 7 0.09 SIDE_CHAIN REMARK 500 C A 10 0.09 SIDE_CHAIN REMARK 500 C A 11 0.08 SIDE_CHAIN REMARK 500 G A 12 0.07 SIDE_CHAIN REMARK 500 C A 14 0.09 SIDE_CHAIN REMARK 500 C A 15 0.10 SIDE_CHAIN REMARK 500 A A 16 0.11 SIDE_CHAIN REMARK 500 C A 17 0.09 SIDE_CHAIN REMARK 500 U A 18 0.09 SIDE_CHAIN REMARK 500 A A 23 0.05 SIDE_CHAIN REMARK 500 G A 29 0.08 SIDE_CHAIN REMARK 500 G A 30 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YG3 RELATED DB: PDB REMARK 900 THE SAME SEQUENCE, 20 LOWEST ENERGY STRUCTURES DBREF 1YG4 A 3 30 PDB 1YG4 1YG4 3 30 SEQRES 1 A 28 A G U G G CH G C C G A C C SEQRES 2 A 28 A C U U A A A A A C A C C SEQRES 3 A 28 G G MODRES 1YG4 CH A 8 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE HET CH A 8 32 HETNAM CH N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 CH C9 H15 N3 O8 P 1+ LINK O3' G A 7 P CH A 8 1555 1555 1.57 LINK O3' CH A 8 P G A 9 1555 1555 1.62 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 MASTER 202 0 1 0 0 0 0 6 0 0 0 3 END