HEADER RNA 21-JUL-00 1FEQ TITLE NMR SOLUTION STRUCTURE OF THE ANTICODON OF TRNA(LYS3) WITH T6A TITLE 2 MODIFICATION AT POSITION 37 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*CP*AP*GP*AP*CP*UP*UP*UP*UP*(T6A) COMPND 3 P*AP*UP*CP*UP*GP*C)-3'; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: ANTICODON (RESIDUES 27-43) OF TRNA(LYS3) WITH T6A COMPND 6 MODIFICATION AT POSITION 37; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE OF TRNA(LYS3) WITH TERMINAL BASE PAIR SOURCE 4 REPLACED WITH GC TO ENHANCE SYNTHESIS YIELD AND STABILITY KEYWDS TRNA, ANTICODON STEM LOOP, TRNA DOMAIN, RNA HAIRPIN, T6A, RNA EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR J.W.STUART,Z.GDANIEC,R.H.GUENTHER,M.MARSZALEK,E.SOCHACKA, AUTHOR 2 A.MALKIEWICZ,P.F.AGRIS REVDAT 6 22-MAY-24 1FEQ 1 REMARK REVDAT 5 23-FEB-22 1FEQ 1 REMARK LINK REVDAT 4 24-FEB-09 1FEQ 1 VERSN REVDAT 3 01-APR-03 1FEQ 1 JRNL REVDAT 2 13-DEC-00 1FEQ 1 TITLE COMPND SOURCE JRNL REVDAT 1 22-NOV-00 1FEQ 0 JRNL AUTH J.W.STUART,Z.GDANIEC,R.GUENTHER,M.MARSZALEK,E.SOCHACKA, JRNL AUTH 2 A.MALKIEWICZ,P.F.AGRIS JRNL TITL FUNCTIONAL ANTICODON ARCHITECTURE OF HUMAN TRNALYS3 INCLUDES JRNL TITL 2 DISRUPTION OF INTRALOOP HYDROGEN BONDING BY THE NATURALLY JRNL TITL 3 OCCURRING AMINO ACID MODIFICATION, T6A. JRNL REF BIOCHEMISTRY V. 39 13396 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 11063577 JRNL DOI 10.1021/BI0013039 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 98, DISCOVER 98 REMARK 3 AUTHORS : MSI (FELIX), MSI (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 272 RESTRAINTS, 207 NOE-DERIVED, 13 H REMARK 3 -BOND, 52 DIHEDRAL ANGLE. CHI TORSION WAS LEFT UNRESTRAINED REMARK 3 ALTHOUGH LIKELY ANTI FOR ALL RESIDUES. REMARK 4 REMARK 4 1FEQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-00. REMARK 100 THE DEPOSITION ID IS D_1000011520. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 289 REMARK 210 PH : 5.6 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.2 MM RNA, 10 MM CACODYLATE REMARK 210 BUFFER, PH 5.6, 0.1 MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : GLOBAL FOLD BY DISTANCE REMARK 210 GEOMETRY. REFINEMENT BY REMARK 210 SIMULATED ANNEALING USING THE REMARK 210 AMBER FORCEFIELD REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES 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 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 2 G A 30 C5' G A 30 C4' 0.073 REMARK 500 2 C A 32 N1 C A 32 C6 0.065 REMARK 500 2 A A 38 N1 A A 38 C2 0.054 REMARK 500 3 C A 32 N1 C A 32 C6 0.065 REMARK 500 4 C A 32 N1 C A 32 C6 0.065 REMARK 500 4 A A 38 N1 A A 38 C2 0.054 REMARK 500 5 C A 32 N1 C A 32 C6 0.065 REMARK 500 6 C A 32 N1 C A 32 C6 0.065 REMARK 500 7 G A 30 C5' G A 30 C4' 0.084 REMARK 500 7 C A 32 N1 C A 32 C6 0.064 REMARK 500 8 G A 30 C5' G A 30 C4' 0.079 REMARK 500 8 C A 32 N1 C A 32 C6 0.065 REMARK 500 9 C A 32 N1 C A 32 C6 0.066 REMARK 500 10 G A 30 C5' G A 30 C4' 0.077 REMARK 500 10 C A 32 N1 C A 32 C6 0.067 REMARK 500 10 A A 38 N1 A A 38 C2 0.054 REMARK 500 11 C A 32 N1 C A 32 C6 0.067 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 A A 29 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 A A 31 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 A A 38 C2 - N3 - C4 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 U A 41 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 A A 29 C1' - O4' - C4' ANGL. DEV. = -4.2 DEGREES REMARK 500 2 A A 29 O4' - C1' - N9 ANGL. DEV. = 8.3 DEGREES REMARK 500 2 G A 30 C5' - C4' - O4' ANGL. DEV. = 11.8 DEGREES REMARK 500 2 G A 30 C3' - C2' - C1' ANGL. DEV. = 5.6 DEGREES REMARK 500 2 G A 30 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 A A 31 O4' - C4' - C3' ANGL. DEV. = -8.3 DEGREES REMARK 500 2 A A 31 C5' - C4' - O4' ANGL. DEV. = 7.6 DEGREES REMARK 500 2 A A 31 C1' - O4' - C4' ANGL. DEV. = -7.4 DEGREES REMARK 500 2 A A 31 C3' - C2' - C1' ANGL. DEV. = -4.4 DEGREES REMARK 500 2 C A 32 C6 - N1 - C1' ANGL. DEV. = 8.5 DEGREES REMARK 500 2 C A 32 C2 - N1 - C1' ANGL. DEV. = -6.9 DEGREES REMARK 500 2 U A 34 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 U A 35 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 A A 38 C2 - N3 - C4 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 C A 40 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 2 U A 41 C5' - C4' - O4' ANGL. DEV. = 5.4 DEGREES REMARK 500 3 C A 28 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 A A 29 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 G A 30 C5' - C4' - O4' ANGL. DEV. = 9.4 DEGREES REMARK 500 3 G A 30 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 3 A A 31 O4' - C4' - C3' ANGL. DEV. = -8.2 DEGREES REMARK 500 3 A A 31 C5' - C4' - O4' ANGL. DEV. = 7.2 DEGREES REMARK 500 3 A A 31 C1' - O4' - C4' ANGL. DEV. = -5.9 DEGREES REMARK 500 3 C A 32 C6 - N1 - C1' ANGL. DEV. = 8.2 DEGREES REMARK 500 3 C A 32 C2 - N1 - C1' ANGL. DEV. = -6.7 DEGREES REMARK 500 3 U A 35 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.1 DEGREES REMARK 500 3 A A 38 C2 - N3 - C4 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 C A 40 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 U A 41 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 G A 27 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 G A 30 C5' - C4' - O4' ANGL. DEV. = 9.3 DEGREES REMARK 500 4 A A 31 O4' - C4' - C3' ANGL. DEV. = -8.1 DEGREES REMARK 500 4 A A 31 C5' - C4' - O4' ANGL. DEV. = 6.9 DEGREES REMARK 500 4 A A 31 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 4 C A 32 C6 - N1 - C1' ANGL. DEV. = 7.6 DEGREES REMARK 500 4 U A 35 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.1 DEGREES REMARK 500 4 A A 38 C2 - N3 - C4 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 C A 40 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 4 U A 41 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 C A 28 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 5 A A 29 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 5 G A 30 C5' - C4' - O4' ANGL. DEV. = 8.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 142 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 U A 33 0.11 SIDE CHAIN REMARK 500 1 U A 39 0.06 SIDE CHAIN REMARK 500 2 G A 27 0.05 SIDE CHAIN REMARK 500 2 A A 31 0.10 SIDE CHAIN REMARK 500 2 C A 32 0.07 SIDE CHAIN REMARK 500 2 U A 33 0.11 SIDE CHAIN REMARK 500 2 U A 39 0.12 SIDE CHAIN REMARK 500 2 C A 40 0.09 SIDE CHAIN REMARK 500 2 U A 41 0.07 SIDE CHAIN REMARK 500 3 A A 31 0.08 SIDE CHAIN REMARK 500 3 C A 32 0.07 SIDE CHAIN REMARK 500 3 U A 33 0.10 SIDE CHAIN REMARK 500 3 U A 39 0.07 SIDE CHAIN REMARK 500 3 U A 41 0.10 SIDE CHAIN REMARK 500 3 G A 42 0.09 SIDE CHAIN REMARK 500 4 G A 27 0.06 SIDE CHAIN REMARK 500 4 A A 31 0.09 SIDE CHAIN REMARK 500 4 C A 32 0.07 SIDE CHAIN REMARK 500 4 U A 33 0.09 SIDE CHAIN REMARK 500 4 U A 39 0.09 SIDE CHAIN REMARK 500 4 U A 41 0.09 SIDE CHAIN REMARK 500 4 G A 42 0.07 SIDE CHAIN REMARK 500 5 A A 29 0.06 SIDE CHAIN REMARK 500 5 A A 31 0.07 SIDE CHAIN REMARK 500 5 C A 32 0.11 SIDE CHAIN REMARK 500 5 U A 33 0.10 SIDE CHAIN REMARK 500 5 C A 40 0.14 SIDE CHAIN REMARK 500 5 U A 41 0.09 SIDE CHAIN REMARK 500 5 G A 42 0.06 SIDE CHAIN REMARK 500 6 A A 31 0.10 SIDE CHAIN REMARK 500 6 U A 34 0.11 SIDE CHAIN REMARK 500 6 U A 39 0.08 SIDE CHAIN REMARK 500 6 C A 40 0.08 SIDE CHAIN REMARK 500 6 G A 42 0.07 SIDE CHAIN REMARK 500 7 G A 30 0.07 SIDE CHAIN REMARK 500 7 A A 31 0.06 SIDE CHAIN REMARK 500 7 C A 32 0.10 SIDE CHAIN REMARK 500 7 A A 38 0.06 SIDE CHAIN REMARK 500 7 U A 39 0.07 SIDE CHAIN REMARK 500 7 C A 40 0.08 SIDE CHAIN REMARK 500 7 U A 41 0.06 SIDE CHAIN REMARK 500 7 G A 42 0.08 SIDE CHAIN REMARK 500 8 A A 31 0.10 SIDE CHAIN REMARK 500 8 C A 32 0.08 SIDE CHAIN REMARK 500 8 U A 39 0.07 SIDE CHAIN REMARK 500 8 C A 40 0.07 SIDE CHAIN REMARK 500 8 U A 41 0.13 SIDE CHAIN REMARK 500 8 G A 42 0.08 SIDE CHAIN REMARK 500 9 A A 31 0.07 SIDE CHAIN REMARK 500 9 C A 32 0.06 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 64 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BZ2 RELATED DB: PDB REMARK 900 CONTAINS SAME ANTICODON AT PH 7 WITH NO T6A MODIFICATION REMARK 900 RELATED ID: 1BZ3 RELATED DB: PDB REMARK 900 CONTAINS SAME ANTICODON AT PH 5 WITH NO T6A MODIFICATION DBREF 1FEQ A 27 43 PDB 1FEQ 1FEQ 27 43 SEQRES 1 A 17 G C A G A C U U U U T6A A U SEQRES 2 A 17 C U G C MODRES 1FEQ T6A A 37 A HET T6A A 37 49 HETNAM T6A N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL) HETNAM 2 T6A CARBAMOYL]THREONINE-5'-MONOPHOSPHATE HETSYN T6A N-(NEBULARIN-6-YLCARBAMOYL)-L-THREONINE-5'- HETSYN 2 T6A MONOPHOSPHATE FORMUL 1 T6A C15 H21 N6 O11 P 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 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