HEADER RNA 23-MAY-02 1LUX TITLE NMR SOLUTION STRUCTURE OF THE ANTICODON OF YEAST TRNA-PHE WITH 3 TITLE 2 MODIFICATIONS (OMC32 OMG34 M5C40) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*CP*CP*AP*GP*AP*(OMC)P*UP*(OMG)P*AP*AP*GP*AP*UP*(5MC) COMPND 3 P*UP*GP*G)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: ANTICODON (RESIDUES 27-43) OF TRNA-PHE WITH THREE COMPND 7 MODIFIED RESIDUES (OMC AT POSITION 32, OMG AT 34, M5C AT POSITION 40) SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE WITH NATURALLY OCCURRING MODIFICATIONS SOURCE 4 SYNTHESIZED USING PHOSPHORAMIDITE CHEMISTRY. KEYWDS TRNA, ANTICODON STEM LOOP, TRNA DOMAIN, RNA HAIRPIN, 2'-O-METHYL, KEYWDS 2 M5C, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.W.STUART,K.M.KOSHLAP,R.H.GUENTHER,P.F.AGRIS REVDAT 4 23-FEB-22 1LUX 1 REMARK LINK REVDAT 3 24-FEB-09 1LUX 1 VERSN REVDAT 2 16-DEC-03 1LUX 1 JRNL REVDAT 1 09-SEP-03 1LUX 0 JRNL AUTH J.W.STUART,K.M.KOSHLAP,R.GUENTHER,P.F.AGRIS JRNL TITL NATURALLY-OCCURRING MODIFICATION RESTRICTS THE ANTICODON JRNL TITL 2 DOMAIN CONFORMATIONAL SPACE OF TRNA(PHE). JRNL REF J.MOL.BIOL. V. 334 901 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 14643656 JRNL DOI 10.1016/J.JMB.2003.09.058 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR, DISCOVER 98 REMARK 3 AUTHORS : BRUKER (XWINNMR), ACCELRYS (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 271 RESTRAINTS (258 NOE-DERIVED, 13 H REMARK 3 -BOND), 95 DIHEDRAL ANGLE REMARK 4 REMARK 4 1LUX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1000016296. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.60 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.6 MM RNA, 10 MM CACODYLATE REMARK 210 BUFFER, PH 5.6, 0.1 MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY 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 : FELIX 98 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 : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 9 A A 38 N1 A A 38 C2 0.055 REMARK 500 10 A A 38 N1 A A 38 C2 0.055 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 C A 27 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 U A 33 C5' - C4' - O4' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 U A 33 C3' - C2' - C1' ANGL. DEV. = 6.3 DEGREES REMARK 500 1 U A 33 O4' - C1' - N1 ANGL. DEV. = 7.6 DEGREES REMARK 500 1 OMG A 34 C3' - O3' - P ANGL. DEV. = 11.3 DEGREES REMARK 500 1 A A 35 O3' - P - O5' ANGL. DEV. = -11.8 DEGREES REMARK 500 1 A A 35 C5' - C4' - O4' ANGL. DEV. = 8.0 DEGREES REMARK 500 1 A A 35 O4' - C1' - N9 ANGL. DEV. = 7.7 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. = 4.1 DEGREES REMARK 500 1 G A 43 O4' - C1' - N9 ANGL. DEV. = 7.5 DEGREES REMARK 500 2 C A 27 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 A A 35 N9 - C1' - C2' ANGL. DEV. = 9.9 DEGREES REMARK 500 2 A A 36 O4' - C1' - N9 ANGL. DEV. = 7.1 DEGREES REMARK 500 2 A A 38 C5' - C4' - O4' ANGL. DEV. = 6.1 DEGREES REMARK 500 2 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 A A 38 C2 - N3 - C4 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 U A 41 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 G A 43 O4' - C1' - N9 ANGL. DEV. = 7.4 DEGREES REMARK 500 3 C A 27 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 A A 35 C5' - C4' - O4' ANGL. DEV. = 5.5 DEGREES REMARK 500 3 A A 35 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 G A 37 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 A A 38 C5' - C4' - O4' ANGL. DEV. = 6.4 DEGREES REMARK 500 3 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.3 DEGREES REMARK 500 3 A A 38 C2 - N3 - C4 ANGL. DEV. = 4.1 DEGREES REMARK 500 3 U A 41 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 G A 43 O4' - C1' - N9 ANGL. DEV. = 7.2 DEGREES REMARK 500 4 C A 27 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 4 OMG A 34 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 4 A A 35 C5' - C4' - O4' ANGL. DEV. = 7.6 DEGREES REMARK 500 4 A A 35 O4' - C1' - N9 ANGL. DEV. = 7.5 DEGREES REMARK 500 4 A A 36 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 4 A A 38 C5' - C4' - O4' ANGL. DEV. = 5.5 DEGREES REMARK 500 4 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.3 DEGREES REMARK 500 4 A A 38 C2 - N3 - C4 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 U A 39 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 C A 27 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 A A 35 O4' - C1' - N9 ANGL. DEV. = 8.8 DEGREES REMARK 500 5 A A 36 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 G A 37 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 5 A A 38 C5' - C4' - O4' ANGL. DEV. = 5.5 DEGREES REMARK 500 5 A A 38 N1 - C2 - N3 ANGL. DEV. = -5.3 DEGREES REMARK 500 5 A A 38 C2 - N3 - C4 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 G A 43 O4' - C1' - N9 ANGL. DEV. = 7.5 DEGREES REMARK 500 6 C A 27 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 U A 33 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 6 A A 35 C5' - C4' - O4' ANGL. DEV. = 6.5 DEGREES REMARK 500 6 A A 35 O4' - C1' - N9 ANGL. DEV. = 12.2 DEGREES REMARK 500 6 A A 38 C5' - C4' - O4' ANGL. DEV. = 5.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 79 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 A A 29 0.08 SIDE CHAIN REMARK 500 1 A A 31 0.06 SIDE CHAIN REMARK 500 1 A A 35 0.09 SIDE CHAIN REMARK 500 1 U A 41 0.07 SIDE CHAIN REMARK 500 2 U A 33 0.13 SIDE CHAIN REMARK 500 2 A A 35 0.12 SIDE CHAIN REMARK 500 2 U A 41 0.06 SIDE CHAIN REMARK 500 3 C A 27 0.08 SIDE CHAIN REMARK 500 3 A A 31 0.07 SIDE CHAIN REMARK 500 3 U A 33 0.09 SIDE CHAIN REMARK 500 3 A A 35 0.09 SIDE CHAIN REMARK 500 3 A A 36 0.10 SIDE CHAIN REMARK 500 3 G A 37 0.07 SIDE CHAIN REMARK 500 3 U A 41 0.07 SIDE CHAIN REMARK 500 4 A A 31 0.07 SIDE CHAIN REMARK 500 4 U A 33 0.08 SIDE CHAIN REMARK 500 4 A A 35 0.21 SIDE CHAIN REMARK 500 4 G A 43 0.08 SIDE CHAIN REMARK 500 5 G A 30 0.06 SIDE CHAIN REMARK 500 5 A A 31 0.07 SIDE CHAIN REMARK 500 5 U A 33 0.06 SIDE CHAIN REMARK 500 5 A A 35 0.15 SIDE CHAIN REMARK 500 5 G A 37 0.06 SIDE CHAIN REMARK 500 5 A A 38 0.06 SIDE CHAIN REMARK 500 6 C A 27 0.07 SIDE CHAIN REMARK 500 6 A A 31 0.09 SIDE CHAIN REMARK 500 6 U A 33 0.09 SIDE CHAIN REMARK 500 6 A A 35 0.06 SIDE CHAIN REMARK 500 6 G A 37 0.07 SIDE CHAIN REMARK 500 6 G A 43 0.06 SIDE CHAIN REMARK 500 7 C A 27 0.09 SIDE CHAIN REMARK 500 7 A A 29 0.06 SIDE CHAIN REMARK 500 7 A A 31 0.07 SIDE CHAIN REMARK 500 7 U A 33 0.16 SIDE CHAIN REMARK 500 7 A A 36 0.09 SIDE CHAIN REMARK 500 8 C A 28 0.09 SIDE CHAIN REMARK 500 8 A A 31 0.09 SIDE CHAIN REMARK 500 8 G A 37 0.06 SIDE CHAIN REMARK 500 8 A A 38 0.09 SIDE CHAIN REMARK 500 9 A A 31 0.08 SIDE CHAIN REMARK 500 9 U A 33 0.08 SIDE CHAIN REMARK 500 9 A A 36 0.09 SIDE CHAIN REMARK 500 9 G A 42 0.06 SIDE CHAIN REMARK 500 10 A A 31 0.08 SIDE CHAIN REMARK 500 10 U A 33 0.22 SIDE CHAIN REMARK 500 10 G A 37 0.06 SIDE CHAIN REMARK 500 10 A A 38 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LUU RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF THE ANTICODON OF YEAST TRNA-PHE WITH 4 REMARK 900 MODIFICATIONS (OMC32 OMG34 1MG37 5MC40) DBREF 1LUX A 27 43 PDB 1LUX 1LUX 27 43 SEQRES 1 A 17 C C A G A OMC U OMG A A G A U SEQRES 2 A 17 5MC U G G MODRES 1LUX OMC A 32 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 1LUX OMG A 34 G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1LUX 5MC A 40 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE HET OMC A 32 34 HET OMG A 34 37 HET 5MC A 40 34 HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM OMG O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM 5MC 5-METHYLCYTIDINE-5'-MONOPHOSPHATE FORMUL 1 OMC C10 H16 N3 O8 P FORMUL 1 OMG C11 H16 N5 O8 P FORMUL 1 5MC C10 H16 N3 O8 P LINK O3' A A 31 P OMC A 32 1555 1555 1.62 LINK O3' OMC A 32 P U A 33 1555 1555 1.62 LINK O3' U A 33 P OMG A 34 1555 1555 1.63 LINK O3' OMG A 34 P A A 35 1555 1555 1.59 LINK O3' U A 39 P 5MC A 40 1555 1555 1.62 LINK O3' 5MC A 40 P U A 41 1555 1555 1.61 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