HEADER RNA 15-FEB-06 2G1W TITLE NMR STRUCTURE OF THE AQUIFEX AEOLICUS TMRNA PSEUDOKNOT PK1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 R(*GP*GP*GP*GP*UP*GP*GP*CP*UP*CP*CP*CP*CP*UP*AP*AP*CP*AP*GP COMPND 4 *CP*CP*G)-3'; COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE SEQUENCE OF THIS RNA NATURALLY EXISTS SOURCE 4 IN AQUIFEX AEOLICUS (BACTERIA) KEYWDS TMRNA, PK1, PSEUDOKNOT, TRANS-TRANSLATION, NMR EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR S.NONIN-LECOMTE,F.DARDEL 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 JRNL TITL 2 PSEUDOKNOT PK1: NEW INSIGHTS INTO THE RECODING JRNL TITL 3 EVENT OF THE RIBOSOMAL 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 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER, ADAMS,CLORE, DELANO,GROSS, GROSSE- REMARK 3 KUNSTLEVE, JIANG, KUZEWSKI, NILGES, PANNU, READ, REMARK 3 RICE, SIMMONSON, WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A- DYNAMICAL ANNEALING PROTOCOL: 1. REMARK 3 TAMD 30 PS AT 20000K 2. FIRST COOLING STAGE TAMD 40PS 3. REMARK 3 SECOND SLOW COOLING ANNEALING STAGE, RESTRAINED MOLECULAR REMARK 3 DYNAMICS 35PS. 4. 10 CYCLES OF ENERGY MINIMIZATION OF 300 REMARK 3 STEPS EACH. B- ENERGY MINIMIZATION: 1-TAMD 10PS AT 300K, 2- REMARK 3 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 22-FEB-06. REMARK 100 THE RCSB ID CODE IS RCSB036584. 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 REMARK 210 PK1, 50MM NACL, 0.5 MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, HCN, 1H 13C HSQC, REMARK 210 1H 13C CONSTANT TIME HSQC, 1H REMARK 210 13C LONG-RANGE HSQC, HCCH- REMARK 210 TOCSY, HCCH E.COSY, HCC-TOCSY- REMARK 210 CCH-E.COSY, 3D NOESY-HSQC, REMARK 210 HMBC, 1H 15N TROSY, 2JNN HNN- REMARK 210 COSY, 2JNH HNN-COSY, 3D NOESY- REMARK 210 HMBC, 2D 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 : UXNMR 3.1, FELIX 2000.1, REMARK 210 MOLMOL 2K.1 REMARK 210 METHOD USED : CNS DYNAMICAL ANNEALING REMARK 210 PROTOCOL 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 REMARK 210 ENERGY, STRUCTURES WITH THE REMARK 210 LEAST RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2' G A 3 OP1 G A 4 2.13 REMARK 500 O2' G A 7 OP1 C A 8 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 80 0 0 0 0 0 0 6 0 0 0 2 END