HEADER RNA 11-AUG-00 1FL8 TITLE HYPERMODIFIED NUCLEOSIDES IN THE ANTICODON OF TRNALYS STABILIZE A TITLE 2 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 IDENTICAL TO THOSE COMPND 8 FOUND IN THE ANTICODON DOMAIN OF E. COLI TRNA(LYS) INCLUDING MODIFIED COMPND 9 NUCLEOSIDES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS TRNA, ANTICODON, PSEUDOURIDINE, MNM5S2U, T6A, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.SUNDARAM,P.C.DURANT,D.R.DAVIS REVDAT 3 23-FEB-22 1FL8 1 REMARK LINK 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 TRNALYS JRNL TITL 2 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1B, DISCOVER REMARK 3 AUTHORS : VARIAN (VNMR), MSI (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 123 NOE-DERIVED RESTRAINTS, 15 HYDROGEN REMARK 3 BOND RESTRAINTS, 102 LOWER/UPPER BOUND RESTRAINTS, 161 DIHEDRAL REMARK 3 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 DEPOSITION ID IS D_1000011684. 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 KCL; REMARK 210 50MM NACL; 10MM MGCL2; 1.5MM REMARK 210 NATURAL ABUNDANCE RNA; 10MM REMARK 210 PHOSPHATE BUFFER; 50MM KCL; 50MM REMARK 210 NACL; 10MM MGCL2 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 1H-31P-COSY; REMARK 210 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 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 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: 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 1 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.5 DEGREES REMARK 500 2 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.6 DEGREES REMARK 500 3 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.5 DEGREES REMARK 500 4 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.5 DEGREES REMARK 500 5 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.3 DEGREES REMARK 500 6 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.5 DEGREES REMARK 500 7 C A 32 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 7 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.3 DEGREES REMARK 500 8 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.4 DEGREES REMARK 500 9 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.5 DEGREES REMARK 500 10 C A 32 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 10 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.4 DEGREES REMARK 500 10 PSU A 39 C3' - O3' - P ANGL. DEV. = -7.2 DEGREES REMARK 500 11 C A 32 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 11 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.7 DEGREES REMARK 500 12 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.4 DEGREES REMARK 500 13 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.6 DEGREES REMARK 500 14 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.6 DEGREES REMARK 500 15 U A 33 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 16 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.5 DEGREES REMARK 500 17 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.5 DEGREES REMARK 500 18 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.4 DEGREES REMARK 500 19 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.5 DEGREES REMARK 500 20 U8U A 34 C3' - O3' - P ANGL. DEV. = -7.5 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 NUCLEOSIDES REMARK 900 AT POSITION 34 AND 37. PSEUDOURIDINE IS PRESENT AT POSTION 39 REMARK 900 RELATED ID: 1BZ2 RELATED DB: PDB REMARK 900 THE SAME ANTICODON LOOP SEQUENCE BUT WITHOUT MODIFIED NUCLEOSIDES REMARK 900 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 MODEL 1