HEADER RNA 09-OCT-00 1E95 TITLE SOLUTION STRUCTURE OF THE PSEUDOKNOT OF SRV-1 RNA, INVOLVED TITLE 2 IN RIBOSOMAL FRAMESHIFTING COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-(*GP*CP*GP*GP*CP*CP*AP*GP*CP*UP*CP* COMPND 3 CP*AP*GP*GP*CP*CP*GP*CP*CP*AP*AP*AP*CP* COMPND 4 AP*AP*UP*AP*UP*GP*GP*AP*GP*CP*AP*C)-3'); COMPND 5 CHAIN: A; COMPND 6 FRAGMENT: GAG-PRO FRAMESHIFTING PSEUDOKNOT; COMPND 7 SYNONYM: SRV-1 RNA PSEUDOKNOT; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SIMIAN RETROVIRUS 1; SOURCE 4 ORGANISM_COMMON: SRV-1; SOURCE 5 ORGANISM_TAXID: 11942 KEYWDS RIBONUCLEIC ACID, SRV-1, RNA, PSEUDOKNOT, FRAMESHIFT EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR P.J.A.MICHIELS,A.VERSLEYEN,C.W.A.PLEIJ,C.W.HILBERS,H.A.HEUS REVDAT 2 24-FEB-09 1E95 1 VERSN REVDAT 1 23-AUG-01 1E95 0 JRNL AUTH P.J.A.MICHIELS,A.A.VERSLEIJEN,P.W.VERLAAN, JRNL AUTH 2 C.W.A.PLEIJ,C.W.HILBERS,H.A.HEUS JRNL TITL SOLUTION STRUCTURE OF THE PSEUDOKNOT OF SRV-1 RNA, JRNL TITL 2 INVOLVED IN RIBOSOMAL FRAMESHIFTING JRNL REF J.MOL.BIOL. V. 310 1109 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11501999 JRNL DOI 10.1006/JMBI.2001.4823 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1E95 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-OCT-00. REMARK 100 THE PDBE ID CODE IS EBI-5425. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : 100 MM NACL, 10 MM REMARK 210 K2HPO4/KH2PO4 REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; DQF-COSY; TOCSY; REMARK 210 31P-1H HETCOR; HMQC; REMARK 210 31P-1H HETERO-TOCSY-NOESY; REMARK 210 NOESY-HMQC; HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500; 600; 750 REMARK 210 SPECTROMETER MODEL : DMX600; INOVA 500; INOVA 750 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT REMARK 210 VIOLATIONS, LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 400 REMARK 400 COMPOUND REMARK 400 CHAIN A ENGINEERED MUTATION G2C, C10U, C18G, G35A, REMARK 400 DELTA(G26, C27, U28) 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 1 G A 3 C5' G A 3 C4' 0.044 REMARK 500 1 G A 4 C5' G A 4 C4' 0.043 REMARK 500 1 A A 32 C5' A A 32 C4' 0.043 REMARK 500 1 G A 33 C5' G A 33 C4' 0.044 REMARK 500 2 A A 32 C5' A A 32 C4' 0.046 REMARK 500 2 G A 33 C5' G A 33 C4' 0.042 REMARK 500 3 G A 3 C5' G A 3 C4' 0.042 REMARK 500 3 G A 4 C5' G A 4 C4' 0.042 REMARK 500 3 A A 32 C5' A A 32 C4' 0.043 REMARK 500 3 G A 33 C5' G A 33 C4' 0.043 REMARK 500 4 G A 4 C5' G A 4 C4' 0.042 REMARK 500 4 G A 8 C5' G A 8 C4' 0.044 REMARK 500 4 A A 32 C5' A A 32 C4' 0.044 REMARK 500 5 G A 8 C5' G A 8 C4' 0.044 REMARK 500 5 A A 32 C5' A A 32 C4' 0.045 REMARK 500 5 G A 33 C5' G A 33 C4' 0.043 REMARK 500 6 G A 4 C5' G A 4 C4' 0.045 REMARK 500 6 A A 32 C5' A A 32 C4' 0.043 REMARK 500 7 A A 32 C5' A A 32 C4' 0.044 REMARK 500 7 G A 33 C5' G A 33 C4' 0.043 REMARK 500 8 G A 3 C5' G A 3 C4' 0.043 REMARK 500 8 A A 32 C5' A A 32 C4' 0.044 REMARK 500 9 G A 4 C5' G A 4 C4' 0.044 REMARK 500 9 A A 23 C5' A A 23 C4' 0.049 REMARK 500 9 A A 32 C5' A A 32 C4' 0.044 REMARK 500 10 G A 4 C5' G A 4 C4' 0.043 REMARK 500 10 A A 32 C5' A A 32 C4' 0.044 REMARK 500 10 G A 33 C5' G A 33 C4' 0.045 REMARK 500 10 A A 35 C5' A A 35 C4' 0.050 REMARK 500 11 G A 4 C5' G A 4 C4' 0.043 REMARK 500 11 G A 8 C5' G A 8 C4' 0.045 REMARK 500 11 A A 23 C5' A A 23 C4' 0.051 REMARK 500 11 A A 32 C5' A A 32 C4' 0.042 REMARK 500 11 G A 33 C5' G A 33 C4' 0.043 REMARK 500 12 G A 8 C5' G A 8 C4' 0.046 REMARK 500 12 G A 14 C5' G A 14 C4' 0.042 REMARK 500 12 A A 32 C5' A A 32 C4' 0.044 REMARK 500 12 G A 33 C5' G A 33 C4' 0.043 REMARK 500 13 G A 14 C5' G A 14 C4' 0.042 REMARK 500 13 A A 32 C5' A A 32 C4' 0.043 REMARK 500 13 G A 33 C5' G A 33 C4' 0.043 REMARK 500 13 A A 35 C5' A A 35 C4' 0.052 REMARK 500 14 A A 32 C5' A A 32 C4' 0.043 REMARK 500 14 A A 35 C5' A A 35 C4' 0.046 REMARK 500 15 A A 32 C5' A A 32 C4' 0.045 REMARK 500 15 G A 33 C5' G A 33 C4' 0.043 REMARK 500 15 A A 35 C5' A A 35 C4' 0.050 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 G A 1 C3' - C2' - C1' ANGL. DEV. = 5.7 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 3 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 3 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 G A 4 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 A A 7 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 A A 7 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 8 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 U A 10 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 A A 13 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 13 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 14 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 15 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 18 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 G A 18 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 A A 21 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 A A 21 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 A A 22 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 A A 22 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 23 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 23 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 25 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 25 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 26 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 A A 26 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 A A 28 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A A 28 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 G A 30 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 G A 30 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 31 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES REMARK 500 1 G A 31 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 G A 31 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 A A 32 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 32 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 G A 33 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 33 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 33 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 A A 35 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 35 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 G A 1 C3' - C2' - C1' ANGL. DEV. = 5.8 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 3 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 696 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 C A 6 0.06 SIDE CHAIN REMARK 500 3 C A 6 0.06 SIDE CHAIN REMARK 500 10 C A 6 0.07 SIDE CHAIN REMARK 500 15 C A 6 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1E95 A 1 36 EMBL M11841 RESIVRV1 2337 2373 SEQADV 1E95 C A 2 EMBL M11841 G 2338 ENGINEERED SEQADV 1E95 U A 10 EMBL M11841 C 2346 ENGINEERED SEQADV 1E95 G A 18 EMBL M11841 C 2354 ENGINEERED SEQADV 1E95 A A 35 EMBL M11841 G 2374 ENGINEERED SEQADV 1E95 A EMBL M11841 G 2363 DELETION SEQADV 1E95 A EMBL M11841 C 2364 DELETION SEQADV 1E95 A EMBL M11841 U 2365 DELETION SEQADV 1E95 A A 32 EMBL M11841 G 2371 CONFLICT SEQADV 1E95 C A 36 EMBL M11841 G 2375 CONFLICT SEQRES 1 A 36 G C G G C C A G C U C C A SEQRES 2 A 36 G G C C G C C A A A C A A SEQRES 3 A 36 U A U G G A G C A 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