HEADER RNA 11-AUG-00 1FL8 TITLE HYPERMODIFIED NUCLEOSIDES IN THE ANTICODON OF TRNALYS TITLE 2 STABILIZE A CANONICAL U-TURN STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTICODON DOMAIN OF TRNA(LYS); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 17-MER TRNA(LYS) ANTICODON DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: RESIDUES 30-40 (TRNA NUMBERING) ARE COMPND 8 IDENTICAL TO THOSE FOUND IN THE ANTICODON DOMAIN OF E. COMPND 9 COLI TRNA(LYS) INCLUDING MODIFIED NUCLEOSIDES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS TRNA, ANTICODON, PSEUDOURIDINE, MNM5S2U, T6A EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.SUNDARAM,P.C.DURANT,D.R.DAVIS REVDAT 2 24-FEB-09 1FL8 1 VERSN REVDAT 1 16-OCT-00 1FL8 0 JRNL AUTH M.SUNDARAM,P.C.DURANT,D.R.DAVIS JRNL TITL HYPERMODIFIED NUCLEOSIDES IN THE ANTICODON OF JRNL TITL 2 TRNALYS STABILIZE A CANONICAL U-TURN STRUCTURE. JRNL REF BIOCHEMISTRY V. 39 12575 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 11027137 JRNL DOI 10.1021/BI0014655 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER REMARK 3 AUTHORS : MSI REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 123 NOE-DERIVED RESTRAINTS, 15 REMARK 3 HYDROGEN BOND RESTRAINTS, 102 LOWER/UPPER BOUND RESTRAINTS, REMARK 3 161 DIHEDRAL RESTRAINTS, 68 CHIRAL RESTRAINTS REMARK 4 REMARK 4 1FL8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-00. REMARK 100 THE RCSB ID CODE IS RCSB011684. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 285; 303 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : 120MM; 120MM REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5MM NATURAL ABUNDANCE RNA; REMARK 210 10MM PHOSPHATE BUFFER; 50MM REMARK 210 KCL; 50MM NACL; 10MM MGCL2; REMARK 210 1.5MM NATURAL ABUNDANCE RNA; REMARK 210 10MM PHOSPHATE BUFFER; 50MM REMARK 210 KCL; 50MM NACL; 10MM MGCL2 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY, 1H-31P- REMARK 210 COSY, 1H-31P-HETERO-TOCSY-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1B, FELIX, DISCOVER REMARK 210 METHOD USED : USED H5-H6 DISTANCES FOR REMARK 210 DISTANCE CALCULATIONS THEN REMARK 210 SIMULATED ANNEALING/MOLECULAR REMARK 210 DYNAMICS IN VACUO THEN REMARK 210 RESTRAINED MINIMIZATION IN REMARK 210 VACUO REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 35 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 4 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES AND STANDARD 1H-31P 2D CORRELATION REMARK 210 EXPERIMENTS. 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: 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 32 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 7 C A 32 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 10 C A 32 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 11 C A 32 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 15 U A 33 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BZU RELATED DB: PDB REMARK 900 THE SAME ANTICODON LOOP SEQUENCE BUT WITHOUT MODIFIED REMARK 900 NUCLEOSIDES AT POSITION 34 AND 37. PSEUDOURIDINE IS PRESENT REMARK 900 AT POSTION 39 REMARK 900 RELATED ID: 1BZ2 RELATED DB: PDB REMARK 900 THE SAME ANTICODON LOOP SEQUENCE BUT WITHOUT MODIFIED REMARK 900 NUCLEOSIDES AT POSITION 34, 37 OR 39 DBREF 1FL8 A 27 43 PDB 1FL8 1FL8 27 43 SEQRES 1 A 17 U C A G A C U U8U U U T6A A PSU SEQRES 2 A 17 C U G A MODRES 1FL8 U8U A 34 U MODRES 1FL8 T6A A 37 A MODRES 1FL8 PSU A 39 U PSEUDOURIDINE-5'-MONOPHOSPHATE HET U8U A 34 39 HET T6A A 37 49 HET PSU A 39 30 HETNAM U8U 5-METHYLAMINOMETHYL-2-THIOURIDINE-5'-MONOPHOSPHATE HETNAM T6A N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL) HETNAM 2 T6A CARBAMOYL]THREONINE-5'-MONOPHOSPHATE HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE HETSYN T6A N-(NEBULARIN-6-YLCARBAMOYL)-L-THREONINE-5'- HETSYN 2 T6A MONOPHOSPHATE FORMUL 1 U8U C11 H18 N3 O8 P S FORMUL 1 T6A C15 H21 N6 O11 P FORMUL 1 PSU C9 H13 N2 O9 P LINK O3' U A 33 P U8U A 34 1555 1555 1.61 LINK O3' U8U A 34 P U A 35 1555 1555 1.62 LINK O3' U A 36 P T6A A 37 1555 1555 1.62 LINK O3' T6A A 37 P A A 38 1555 1555 1.62 LINK O3' A A 38 P PSU A 39 1555 1555 1.62 LINK O3' PSU A 39 P C A 40 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 93 0 3 0 0 0 0 6 0 0 0 2 END