HEADER RNA 13-NOV-17 6EZ0 TITLE SPECIFIC PHOSPHOROTHIOATE SUBSTITUTION WITHIN DOMAIN 6 OF A GROUP II TITLE 2 INTRON RIBOZYME LEADS TO CHANGES IN LOCAL STRUCTURE AND METAL ION TITLE 3 BINDING COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (27-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 4 ORGANISM_TAXID: 4932 KEYWDS THIOPHOSPHATE GROUP II INTRON BRANCH-ADENOSINE HAIRPIN TETRALOOP, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.C.ERAT,E.BESIC,M.OBERHUBER,S.JOHANNSEN,R.K.O.SIGEL REVDAT 4 14-JUN-23 6EZ0 1 REMARK REVDAT 3 08-MAY-19 6EZ0 1 REMARK REVDAT 2 17-JAN-18 6EZ0 1 JRNL REVDAT 1 03-JAN-18 6EZ0 0 JRNL AUTH M.C.ERAT,E.BESIC,M.OBERHUBER,S.JOHANNSEN,R.K.O.SIGEL JRNL TITL SPECIFIC PHOSPHOROTHIOATE SUBSTITUTION WITHIN DOMAIN 6 OF A JRNL TITL 2 GROUP II INTRON RIBOZYME LEADS TO CHANGES IN LOCAL STRUCTURE JRNL TITL 3 AND METAL ION BINDING. JRNL REF J. BIOL. INORG. CHEM. V. 23 167 2018 JRNL REFN ESSN 1432-1327 JRNL PMID 29218637 JRNL DOI 10.1007/S00775-017-1519-3 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.C.ERAT,O.ZERBE,T.FOX,R.K.SIGEL REMARK 1 TITL SOLUTION STRUCTURE OF DOMAIN 6 FROM A SELF-SPLICING GROUP II REMARK 1 TITL 2 INTRON RIBOZYME: A MG(2+) BINDING SITE IS LOCATED CLOSE TO REMARK 1 TITL 3 THE STACKED BRANCH ADENOSINE. REMARK 1 REF CHEMBIOCHEM V. 8 306 2007 REMARK 1 REFN ISSN 1439-4227 REMARK 1 PMID 17200997 REMARK 1 DOI 10.1002/CBIC.200600459 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6EZ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007478. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 275 REMARK 210 PH : 6.7; 6.7 REMARK 210 IONIC STRENGTH : 50; 50 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 2 MM ALPHA-THIO-D6-27, 100% D2O; REMARK 210 0.7 MM NA ALPHA-THIO-D6-27, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 2D 1H- REMARK 210 13C HSQC AROMATIC 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 : XPLOR-NIH, SPARKY 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 : 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 KCAL/MOL 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 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AHT RELATED DB: PDB REMARK 900 THE SAME SEQUENCE BUT WITHOUT THIPPHOSPHATES REMARK 900 RELATED ID: 34199 RELATED DB: BMRB REMARK 900 SPECIFIC PHOSPHOROTHIOATE SUBSTITUTION WITHIN DOMAIN 6 OF A GROUP REMARK 900 II INTRON RIBOZYME LEADS TO CHANGES IN LOCAL STRUCTURE AND METAL REMARK 900 ION BINDING DBREF 6EZ0 A 1 27 PDB 6EZ0 6EZ0 1 27 SEQRES 1 A 27 G G A G C G G G G G U37 G U37 SEQRES 2 A 27 A A A C C U37 A U37 C G C U37 C SEQRES 3 A 27 C HET U37 A 11 30 HET U37 A 13 30 HET U37 A 19 30 HET U37 A 21 30 HET U37 A 25 30 HETNAM U37 URIDINE 5'-MONOTHIOPHOSPHATE FORMUL 1 U37 5(C9 H13 N2 O8 P S) LINK O3' G A 10 P U37 A 11 1555 1555 1.61 LINK O3' U37 A 11 P G A 12 1555 1555 1.61 LINK O3' G A 12 P U37 A 13 1555 1555 1.61 LINK O3' U37 A 13 P A A 14 1555 1555 1.61 LINK O3' C A 18 P U37 A 19 1555 1555 1.61 LINK O3' U37 A 19 P A A 20 1555 1555 1.61 LINK O3' A A 20 P U37 A 21 1555 1555 1.61 LINK O3' U37 A 21 P C A 22 1555 1555 1.61 LINK O3' C A 24 P U37 A 25 1555 1555 1.61 LINK O3' U37 A 25 P C A 26 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