HEADER RNA 04-MAR-98 1A60 TITLE NMR STRUCTURE OF A CLASSICAL PSEUDOKNOT: INTERPLAY OF SINGLE-AND TITLE 2 DOUBLE-STRANDED RNA, 24 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYMV PSEUDOKNOT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ACCEPTOR ARM OF TYMV TRNA-LIKE STRUCTURE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TURNIP YELLOW MOSAIC VIRUS; SOURCE 3 ORGANISM_TAXID: 12154 KEYWDS RNA, PSEUDOKNOT, TYMV, RIBONUCLEIC ACID EXPDTA SOLUTION NMR NUMMDL 24 AUTHOR M.H.KOLK,M.VAN DER GRAAF,S.S.WIJMENGA,C.W.A.PLEIJ,H.A.HEUS, AUTHOR 2 C.W.HILBERS REVDAT 5 22-MAY-24 1A60 1 REMARK REVDAT 4 16-FEB-22 1A60 1 REMARK REVDAT 3 24-FEB-09 1A60 1 VERSN REVDAT 2 01-APR-03 1A60 1 JRNL REVDAT 1 27-MAY-98 1A60 0 JRNL AUTH M.H.KOLK,M.VAN DER GRAAF,S.S.WIJMENGA,C.W.PLEIJ,H.A.HEUS, JRNL AUTH 2 C.W.HILBERS JRNL TITL NMR STRUCTURE OF A CLASSICAL PSEUDOKNOT: INTERPLAY OF JRNL TITL 2 SINGLE- AND DOUBLE-STRANDED RNA. JRNL REF SCIENCE V. 280 434 1998 JRNL REFN ISSN 0036-8075 JRNL PMID 9545221 JRNL DOI 10.1126/SCIENCE.280.5362.434 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: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 1A60 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170435. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 13C-EDITED/ XFILTERED)NOESY; REMARK 210 TOCSY; (31P SPIN ECHO DIFFERENCE) REMARK 210 CTHSQC; PCH; HCCH-TOCSY; CT- REMARK 210 TOCSY-HSQC; HNCCCH REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ; 500 MHZ; 600 MHZ; 750 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : UNITY; AM; AMX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.851 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS/ REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 140 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 24 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATIONS 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 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 O2' U A 22 H5'' U A 23 1.31 REMARK 500 HO2' C A 21 O5' U A 22 1.35 REMARK 500 O2' C A 21 H42 C A 37 1.40 REMARK 500 H2' G A 39 N7 A A 40 1.40 REMARK 500 H1' U A 22 OP1 U A 24 1.47 REMARK 500 N3 C A 6 H41 C A 11 1.49 REMARK 500 H61 A A 4 O4 U A 14 1.51 REMARK 500 O2' C A 34 H5' A A 35 1.54 REMARK 500 O2' C A 8 H8 A A 9 1.56 REMARK 500 H41 C A 18 O6 G A 32 1.58 REMARK 500 O6 G A 1 H41 C A 17 1.59 REMARK 500 O2 C A 20 N1 A A 35 2.16 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 1 A A 35 C8 A A 35 N9 -0.051 REMARK 500 1 A A 40 C2' A A 40 C1' -0.050 REMARK 500 2 A A 40 C2' A A 40 C1' -0.054 REMARK 500 6 A A 4 C2' A A 4 C1' -0.052 REMARK 500 8 A A 35 C8 A A 35 N9 -0.048 REMARK 500 9 A A 4 C2' A A 4 C1' -0.051 REMARK 500 10 A A 4 C2' A A 4 C1' -0.053 REMARK 500 12 A A 40 C2' A A 40 C1' -0.053 REMARK 500 13 A A 40 C2' A A 40 C1' -0.050 REMARK 500 14 A A 35 C8 A A 35 N9 -0.049 REMARK 500 15 C A 16 C2' C A 16 C1' -0.048 REMARK 500 16 A A 40 C2' A A 40 C1' -0.048 REMARK 500 17 A A 35 C8 A A 35 N9 -0.049 REMARK 500 19 A A 35 C8 A A 35 N9 -0.049 REMARK 500 20 A A 4 C2' A A 4 C1' -0.052 REMARK 500 21 A A 35 C8 A A 35 N9 -0.056 REMARK 500 21 A A 40 C2' A A 40 C1' -0.052 REMARK 500 22 A A 35 C8 A A 35 N9 -0.057 REMARK 500 23 A A 35 C8 A A 35 N9 -0.050 REMARK 500 23 A A 40 C2' A A 40 C1' -0.052 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 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 G A 5 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 5 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 C A 16 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 C A 26 C5' - C4' - O4' ANGL. DEV. = 6.8 DEGREES REMARK 500 1 C A 26 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 G A 28 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 28 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 A A 29 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 30 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 G A 30 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 31 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 31 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 32 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 G A 32 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 A A 35 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 C A 37 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 G A 38 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 38 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 39 C3' - C2' - C1' ANGL. DEV. = 5.7 DEGREES REMARK 500 1 G A 39 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 G A 39 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 39 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 1 A A 40 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 A A 40 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 41 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 44 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 G A 2 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 G A 5 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 5 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 C A 16 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 G A 28 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 826 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 1 0.07 SIDE CHAIN REMARK 500 1 A A 4 0.06 SIDE CHAIN REMARK 500 1 G A 5 0.05 SIDE CHAIN REMARK 500 1 C A 13 0.07 SIDE CHAIN REMARK 500 1 C A 15 0.06 SIDE CHAIN REMARK 500 1 C A 17 0.06 SIDE CHAIN REMARK 500 1 C A 19 0.06 SIDE CHAIN REMARK 500 1 A A 29 0.06 SIDE CHAIN REMARK 500 1 G A 32 0.06 SIDE CHAIN REMARK 500 1 G A 38 0.05 SIDE CHAIN REMARK 500 1 G A 39 0.07 SIDE CHAIN REMARK 500 2 G A 1 0.07 SIDE CHAIN REMARK 500 2 G A 3 0.05 SIDE CHAIN REMARK 500 2 G A 5 0.05 SIDE CHAIN REMARK 500 2 C A 13 0.06 SIDE CHAIN REMARK 500 2 C A 15 0.07 SIDE CHAIN REMARK 500 2 C A 20 0.06 SIDE CHAIN REMARK 500 2 C A 26 0.06 SIDE CHAIN REMARK 500 2 A A 29 0.06 SIDE CHAIN REMARK 500 2 G A 30 0.05 SIDE CHAIN REMARK 500 2 G A 31 0.05 SIDE CHAIN REMARK 500 2 G A 32 0.05 SIDE CHAIN REMARK 500 2 G A 38 0.05 SIDE CHAIN REMARK 500 2 G A 39 0.05 SIDE CHAIN REMARK 500 3 G A 3 0.05 SIDE CHAIN REMARK 500 3 A A 4 0.06 SIDE CHAIN REMARK 500 3 G A 5 0.05 SIDE CHAIN REMARK 500 3 C A 13 0.07 SIDE CHAIN REMARK 500 3 C A 15 0.06 SIDE CHAIN REMARK 500 3 C A 16 0.07 SIDE CHAIN REMARK 500 3 C A 18 0.06 SIDE CHAIN REMARK 500 3 C A 19 0.06 SIDE CHAIN REMARK 500 3 C A 20 0.06 SIDE CHAIN REMARK 500 3 C A 26 0.06 SIDE CHAIN REMARK 500 3 C A 27 0.06 SIDE CHAIN REMARK 500 3 A A 29 0.05 SIDE CHAIN REMARK 500 3 G A 30 0.05 SIDE CHAIN REMARK 500 3 G A 31 0.06 SIDE CHAIN REMARK 500 3 G A 32 0.06 SIDE CHAIN REMARK 500 3 C A 34 0.06 SIDE CHAIN REMARK 500 3 G A 38 0.05 SIDE CHAIN REMARK 500 3 A A 40 0.06 SIDE CHAIN REMARK 500 4 G A 3 0.05 SIDE CHAIN REMARK 500 4 A A 4 0.06 SIDE CHAIN REMARK 500 4 G A 5 0.06 SIDE CHAIN REMARK 500 4 C A 13 0.07 SIDE CHAIN REMARK 500 4 C A 15 0.06 SIDE CHAIN REMARK 500 4 C A 16 0.06 SIDE CHAIN REMARK 500 4 C A 17 0.06 SIDE CHAIN REMARK 500 4 C A 18 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 337 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1A60 A 1 44 PDB 1A60 1A60 1 44 SEQRES 1 A 44 G G G A G C U C A A C U C SEQRES 2 A 44 U C C C C C C C U U U U C SEQRES 3 A 44 C G A G G G U C A U C G G SEQRES 4 A 44 A A C C A 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