HEADER RNA 15-FEB-13 2M57 TITLE NMR SOLUTION STRUCTURE OF DOMAIN 5 FROM AZOTOBACTER VINELANDII INTRON TITLE 2 5 AT PH 7.8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA_(35-MER); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GROUP II INTRON DOMAIN 5 (D5); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: AZOTOBACTER VINELANDII; SOURCE 4 ORGANISM_TAXID: 354; SOURCE 5 OTHER_DETAILS: THE SEQUENCE OCCURS NATURALLY AS PART OF INTRON 5 SOURCE 6 FROM A.VINELANDII AND WAS TRANSCRIBED IN VITRO USING T7 RNA SOURCE 7 POLYMERASE FROM A DSDNA TEMPLATE KEYWDS RNA, RIBOZYME, GROUP II INTRON, HAIRPIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.PECHLANER,D.DONGHI,V.ZELENAY,R.K.O.SIGEL REVDAT 2 14-JUN-23 2M57 1 REMARK REVDAT 1 26-FEB-14 2M57 0 JRNL AUTH M.PECHLANER,D.DONGHI,V.ZELENAY,R.K.O.SIGEL JRNL TITL ACID-BASE EQUILIBRIA NEAR NEUTRAL PH IN THE CATALYTIC TRIAD JRNL TITL 2 AND THE BULGE OF DOMAIN 5 OF A BACTERIAL GROUP II INTRON JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2, X-PLOR NIH 2.3 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M57 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000103223. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300; 275; 275; 275 REMARK 210 PH : NULL; 7.8; 5.2; 6.7 REMARK 210 IONIC STRENGTH : 60; 60; 60; 60 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5-1 MM RNA (35-MER), 60 MM REMARK 210 POTASSIUM CHLORIDE, 10 UM EDTA, REMARK 210 100% D2O; 0.5-1 MM RNA (35-MER), REMARK 210 60 MM POTASSIUM CHLORIDE, 10 UM REMARK 210 EDTA, 90% H2O/10% D2O; 0.5-1 MM REMARK 210 [100% 13C; 100% 15N] RNA (35-MER) REMARK 210 , 60 MM POTASSIUM CHLORIDE, 10 REMARK 210 UM EDTA, 100% D2O; 0.5-1 MM [100% REMARK 210 13C; 100% 15N] RNA (35-MER), 60 REMARK 210 MM POTASSIUM CHLORIDE, 10 UM REMARK 210 EDTA, 90% H2O/10% D2O; 0.5-1 MM REMARK 210 [3',4',5',5'',5]-100% 2D RNA (35- REMARK 210 MER), 60 MM POTASSIUM CHLORIDE, REMARK 210 10 UM EDTA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D JNN HNN COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.2, X-PLOR NIH 2.3, MOLMOL, REMARK 210 SPARKY, TOPSPIN 3.0.A, CURVES REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS 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 : 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 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 HO2' G A 4 O5' C A 5 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19039 RELATED DB: BMRB DBREF 2M57 A 1 35 PDB 2M57 2M57 1 35 SEQRES 1 A 35 G G A G C C G U A U G C G SEQRES 2 A 35 G U A G U U C C G C A C G SEQRES 3 A 35 U A C G G A U C U 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