HEADER RNA 15-FEB-06 2G1W TITLE NMR STRUCTURE OF THE AQUIFEX AEOLICUS TMRNA PSEUDOKNOT PK1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*GP*GP*UP*GP*GP*CP*UP*CP*CP*CP*CP*UP*AP*AP*CP*AP COMPND 3 *GP*CP*CP*G)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE SEQUENCE OF THIS RNA NATURALLY EXISTS IN AQUIFEX SOURCE 4 AEOLICUS (BACTERIA) KEYWDS TMRNA, PK1, PSEUDOKNOT, TRANS-TRANSLATION, RNA EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR S.NONIN-LECOMTE,F.DARDEL REVDAT 3 09-MAR-22 2G1W 1 REMARK REVDAT 2 24-FEB-09 2G1W 1 VERSN REVDAT 1 11-APR-06 2G1W 0 JRNL AUTH S.NONIN-LECOMTE,B.FELDEN,F.DARDEL JRNL TITL NMR STRUCTURE OF THE AQUIFEX AEOLICUS TMRNA PSEUDOKNOT PK1: JRNL TITL 2 NEW INSIGHTS INTO THE RECODING EVENT OF THE RIBOSOMAL JRNL TITL 3 TRANS-TRANSLATION. JRNL REF NUCLEIC ACIDS RES. V. 34 1847 2006 JRNL REFN ISSN 0305-1048 JRNL PMID 16595798 JRNL DOI 10.1093/NAR/GKL111 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : UXNMR 3.1, CNS 1.1 REMARK 3 AUTHORS : BRUKER (UXNMR), BRUNGER, ADAMS,CLORE, REMARK 3 DELANO,GROSS, GROSSE-KUNSTLEVE, JIANG, KUZEWSKI, REMARK 3 NILGES, PANNU, READ, RICE, SIMMONSON, WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A- DYNAMICAL ANNEALING PROTOCOL: REMARK 3 1. TAMD 30 PS AT 20000K REMARK 3 2. FIRST COOLING STAGE TAMD 40PS REMARK 3 3. SECOND SLOW COOLING ANNEALING STAGE, RESTRAINED MOLECULAR REMARK 3 DYNAMICS 35PS. REMARK 3 4. 10 CYCLES OF ENERGY MINIMIZATION OF 300 STEPS EACH. REMARK 3 B- ENERGY MINIMIZATION: REMARK 3 1-TAMD 10PS AT 300K, REMARK 3 2- COOLING OVER 9 PS AND 10 POWELL CYCLES OF 800 STEPS EACH. REMARK 4 REMARK 4 2G1W COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000036584. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 293 REMARK 210 PH : 6.3; 6.3 REMARK 210 IONIC STRENGTH : 50MM NACL; 50MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7MM 13C,15N PK1, 50MM NACL, REMARK 210 0.5 MM EDTA; 1MM UNLABELED PK1, REMARK 210 50MM NACL, 0.5 MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; HCN, 1H 13C HSQC, 1H REMARK 210 13C CONSTANT TIME HSQC, 1H 13C REMARK 210 LONG-RANGE HSQC, HCCH-TOCSY, REMARK 210 HCCH E.COSY, HCC-TOCSY-CCH- REMARK 210 E.COSY, 3D NOESY-HSQC; HMBC, 1H REMARK 210 15N TROSY, 2JNN HNN-COSY, 2JNH REMARK 210 HNN-COSY, 3D NOESY-HMBC; 2D REMARK 210 NOESY, TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000.1, MOLMOL 2K.1 REMARK 210 METHOD USED : CNS DYNAMICAL ANNEALING PROTOCOL REMARK 210 FOR NUCLEIC ACIDS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY, STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND ENERGY, REMARK 210 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 : 1 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 DBREF 2G1W A 1 22 PDB 2G1W 2G1W 1 22 SEQRES 1 A 22 G G G G U G G C U C C C C SEQRES 2 A 22 U A A C A G C C G 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