PDB Short entry for 2M23 HEADER RNA 12-DEC-12 2M23 TITLE NMR SOLUTION STRUCTURE OF THE D3'-HAIRPIN OF THE GROUP II INTRON TITLE 2 SC.AI5GAMMA INCLUDING EBS1 BOUND TO IBS1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (29-MER); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: D3'EBS1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: SEQUENCE PRODUCED BY IN-VITRO TRANSCRIPTION FROM A COMPND 8 SYNTHETIC DSDNA TEMPLATE USING T7 RNA-POLYMERASE; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: RNA_(5'-R(*CP*AP*GP*UP*GP*UP*C)-3')_; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: IBS1; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES KEYWDS GROUP II INTRON, RIBOZYME, HAIRPIN, EBS1, IBS1, SPLICING, 5'-SPLICE KEYWDS 2 SITE, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.KRUSCHEL,M.SKILANDAT,R.K.O.SIGEL REVDAT 5 14-JUN-23 2M23 1 REMARK REVDAT 4 16-APR-14 2M23 1 SPRSDE REVDAT 3 12-MAR-14 2M23 1 JRNL REVDAT 2 26-FEB-14 2M23 1 JRNL REVDAT 1 18-DEC-13 2M23 0 SPRSDE 16-APR-14 2M23 2K64 JRNL AUTH D.KRUSCHEL,M.SKILANDAT,R.K.SIGEL JRNL TITL NMR STRUCTURE OF THE 5' SPLICE SITE IN THE GROUP IIB INTRON JRNL TITL 2 SC.AI5 GAMMA--CONFORMATIONAL REQUIREMENTS FOR EXON-INTRON JRNL TITL 3 RECOGNITION. JRNL REF RNA V. 20 295 2014 JRNL REFN ISSN 1355-8382 JRNL PMID 24448450 JRNL DOI 10.1261/RNA.041137.113 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY 3.1, X-PLOR NIH 2.24 REMARK 3 AUTHORS : GODDARD (SPARKY), SCHWIETERS, KUSZEWSKI, TJANDRA REMARK 3 AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M23 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000103111. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 278; 293 REMARK 210 PH : 6.8; 6.8; 6.8 REMARK 210 IONIC STRENGTH : 110; 110; 110 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5-0.9 MM RNA (29-MER), 0.5-0.9 REMARK 210 MM RNA (5'-R(*CP*AP*GP*UP*GP*UP* REMARK 210 C)-3'), 110 MM POTASSIUM REMARK 210 CHLORIDE, 10 UM EDTA, 100% D2O; REMARK 210 0.5-0.9 MM RNA (29-MER), 0.5-0.9 REMARK 210 MM RNA (5'-R(*CP*AP*GP*UP*GP*UP* REMARK 210 C)-3'), 110 MM POTASSIUM REMARK 210 CHLORIDE, 10 UM EDTA, 90% H2O/10% REMARK 210 D2O; 0.5 MM [U-100% 13C; U-100% REMARK 210 15N] RNA (29-MER), 0.5 MM RNA (5' REMARK 210 -R(*CP*AP*GP*UP*GP*UP*C)-3'), REMARK 210 110 MM POTASSIUM CHLORIDE, 10 UM REMARK 210 EDTA, 100% D2O; 0.5 MM [U-100% REMARK 210 13C; U-100% 15N] RNA (29-MER), REMARK 210 0.5 MM RNA (5'-R(*CP*AP*GP*UP*GP* REMARK 210 UP*C)-3'), 110 MM POTASSIUM REMARK 210 CHLORIDE, 10 UM EDTA, 90% H2O/10% REMARK 210 D2O; 0.6 MM [3',4',5',5'',5-100% REMARK 210 2H] RNA (29-MER), 0.6 MM RNA (5' REMARK 210 -R(*CP*AP*GP*UP*GP*UP*C)-3'), REMARK 210 110 MM POTASSIUM CHLORIDE, 10 UM REMARK 210 EDTA, 100% D2O; 0.5 MM [U-100% REMARK 210 13C; U-100% 15N] RNA (29-MER), REMARK 210 0.5 MM RNA (5'-R(*CP*AP*GP*UP*GP* REMARK 210 UP*C)-3'), 110 MM POTASSIUM REMARK 210 CHLORIDE, 10 UM EDTA, 25.6 MG/ML REMARK 210 PF1 PHAGE, 90% 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 15N HSQC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 2D JNN HNN COSY; 1D- REMARK 210 31P; F1,2 X-FILTERED 1H-1H NOESY; REMARK 210 F1,2 X-FILTERED 1H-1H TOCSY 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 : SPARKY 3.1, TOPSPIN 1.3, 2.0, REMARK 210 2.1, DYANA 1.5, CNSSOLVE 1.2, X- REMARK 210 PLOR NIH 2.24 REMARK 210 METHOD USED : MOLECULAR DYNAMICS, TORSION REMARK 210 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 894 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6209 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 O2 U A 12 HO5' C B 59 1.52 REMARK 500 H2' C A 28 O4' C A 29 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K63 RELATED DB: PDB REMARK 900 RELATED ID: 2K64 RELATED DB: PDB REMARK 900 RELATED ID: 2K65 RELATED DB: PDB REMARK 900 RELATED ID: 2K66 RELATED DB: PDB REMARK 900 RELATED ID: 2M1V RELATED DB: PDB REMARK 900 RELATED ID: 2M24 RELATED DB: PDB REMARK 900 RELATED ID: 18893 RELATED DB: BMRB DBREF 2M23 A 1 29 PDB 2M23 2M23 1 29 DBREF 2M23 B 59 65 PDB 2M23 2M23 59 65 SEQRES 1 A 29 G G A G U A U G U A U U G SEQRES 2 A 29 G C A C U G A G C A U A C SEQRES 3 A 29 U C C SEQRES 1 B 7 C A G U G U 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