HEADER RNA 12-AUG-02 1MFK TITLE STRUCTURE OF PROKARYOTIC SECIS MRNA HAIRPIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(P*GP*GP*CP*GP*GP*UP*UP*GP*CP*AP*GP*GP*UP*CP*UP*GP*CP*A COMPND 3 P*CP*CP*GP*CP*C)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: SECIS MRNA HAIRPIN SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE SEQUENCE IS FROM ESCHERICHIA COLI. T7 RNA SOURCE 4 POLYMERASE IN VITRO TRANSCRIPTION. KEYWDS RNA TETRALOOP, (A/U)GNN TETRALOOP FAMILY, SELB, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.FOURMY,E.GUITTET,S.YOSHIZAWA REVDAT 3 23-FEB-22 1MFK 1 REMARK REVDAT 2 24-FEB-09 1MFK 1 VERSN REVDAT 1 13-NOV-02 1MFK 0 JRNL AUTH D.FOURMY,E.GUITTET,S.YOSHIZAWA JRNL TITL STRUCTURE OF PROKARYOTIC SECIS MRNA HAIRPIN AND ITS JRNL TITL 2 INTERACTION WITH ELONGATION FACTOR SELB JRNL REF J.MOL.BIOL. V. 324 137 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12421564 JRNL DOI 10.1016/S0022-2836(02)01030-6 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER, DISCOVER REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC. (DISCOVER), MOLECULAR REMARK 3 SIMULATIONS INC. (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 260 NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 72 DIHEDRAL ANGLE RESTRAINTS REMARK 4 REMARK 4 1MFK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016874. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 275; 278; 288; 293; 303 REMARK 210 PH : 6.4; 6.4; 6.4; 6.4; 6.4 REMARK 210 IONIC STRENGTH : NULL; NULL; NULL; NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM SECIS RNA NON-LABEL; 2MM REMARK 210 PHOSPHATE BUFFER, PH 6.4; 100% REMARK 210 D2O; 1MM SECIS RNA NON-LABEL; REMARK 210 2MM PHOSPHATE BUFFER, PH 6.4; 90% REMARK 210 H2O, 10% D2O; 1MM SECIS RNA U- REMARK 210 15N, 13C; 2MM PHOSPHATE BUFFER, REMARK 210 PH 6.4; 100% D2O; 1MM SECIS RNA REMARK 210 U-15N, 13C; 2MM PHOSPHATE BUFFER, REMARK 210 PH 6.4; 90% H2O, 10% D2O; 1MM REMARK 210 SECIS RNA U-15N; 2MM PHOSPHATE REMARK 210 BUFFER, PH 6.4; 100% D2O; 1MM REMARK 210 SECIS RNA U-15N; 2MM PHOSPHATE REMARK 210 BUFFER, PH 6.4; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AURELIA, XWINNMR, GIFA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 : 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: 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 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 5 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 U A 6 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 U A 7 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 8 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 C A 9 O4' - C1' - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 U A 13 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 1 C A 19 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 C A 20 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 C A 3 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 G A 5 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 G A 12 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 U A 13 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 2 C A 19 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 C A 3 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 G A 5 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 8 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 12 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 U A 13 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 C A 17 O4' - C1' - N1 ANGL. DEV. = 7.9 DEGREES REMARK 500 3 C A 19 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 4 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 4 U A 7 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 U A 13 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 4 C A 17 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 C A 19 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 G A 5 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 5 U A 7 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 G A 12 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 5 U A 15 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 G A 16 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 5 C A 19 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 C A 20 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 5 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 6 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 U A 7 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 6 G A 8 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 6 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 U A 13 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 6 C A 17 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 C A 19 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 172 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 6 0.07 SIDE CHAIN REMARK 500 1 A A 18 0.05 SIDE CHAIN REMARK 500 1 G A 21 0.07 SIDE CHAIN REMARK 500 2 G A 16 0.07 SIDE CHAIN REMARK 500 3 G A 4 0.06 SIDE CHAIN REMARK 500 3 U A 7 0.07 SIDE CHAIN REMARK 500 3 C A 14 0.08 SIDE CHAIN REMARK 500 3 G A 16 0.07 SIDE CHAIN REMARK 500 3 C A 17 0.08 SIDE CHAIN REMARK 500 4 G A 4 0.06 SIDE CHAIN REMARK 500 4 G A 8 0.07 SIDE CHAIN REMARK 500 4 G A 11 0.07 SIDE CHAIN REMARK 500 4 G A 21 0.07 SIDE CHAIN REMARK 500 5 G A 4 0.06 SIDE CHAIN REMARK 500 6 U A 7 0.09 SIDE CHAIN REMARK 500 6 G A 21 0.07 SIDE CHAIN REMARK 500 7 G A 8 0.08 SIDE CHAIN REMARK 500 7 A A 18 0.06 SIDE CHAIN REMARK 500 8 G A 5 0.07 SIDE CHAIN REMARK 500 8 G A 21 0.07 SIDE CHAIN REMARK 500 9 G A 4 0.07 SIDE CHAIN REMARK 500 9 C A 9 0.07 SIDE CHAIN REMARK 500 9 C A 14 0.06 SIDE CHAIN REMARK 500 9 G A 16 0.07 SIDE CHAIN REMARK 500 9 A A 18 0.06 SIDE CHAIN REMARK 500 10 G A 21 0.08 SIDE CHAIN REMARK 500 11 G A 4 0.07 SIDE CHAIN REMARK 500 11 U A 7 0.08 SIDE CHAIN REMARK 500 11 G A 8 0.07 SIDE CHAIN REMARK 500 11 G A 11 0.07 SIDE CHAIN REMARK 500 11 U A 15 0.08 SIDE CHAIN REMARK 500 11 G A 21 0.07 SIDE CHAIN REMARK 500 12 G A 4 0.07 SIDE CHAIN REMARK 500 12 C A 22 0.06 SIDE CHAIN REMARK 500 13 G A 4 0.06 SIDE CHAIN REMARK 500 13 C A 17 0.08 SIDE CHAIN REMARK 500 14 G A 4 0.08 SIDE CHAIN REMARK 500 14 G A 11 0.06 SIDE CHAIN REMARK 500 14 U A 15 0.07 SIDE CHAIN REMARK 500 14 G A 16 0.07 SIDE CHAIN REMARK 500 14 G A 21 0.08 SIDE CHAIN REMARK 500 15 G A 4 0.09 SIDE CHAIN REMARK 500 15 U A 7 0.06 SIDE CHAIN REMARK 500 15 G A 21 0.08 SIDE CHAIN REMARK 500 16 C A 14 0.07 SIDE CHAIN REMARK 500 16 G A 21 0.07 SIDE CHAIN REMARK 500 18 G A 4 0.06 SIDE CHAIN REMARK 500 18 G A 11 0.05 SIDE CHAIN REMARK 500 18 U A 13 0.08 SIDE CHAIN REMARK 500 19 G A 4 0.09 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 55 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1MFK A 1 23 PDB 1MFK 1MFK 1 23 SEQRES 1 A 23 G G C G G U U G C A G G U SEQRES 2 A 23 C U G C A C C G C C 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