HEADER DNA/RNA 07-DEC-12 2M1V TITLE NMR SOLUTION STRUCTURE OF THE D3'-HAIRPIN FROM THE SC.AI5GAMMA GROUP TITLE 2 II INTRON INCLUDING THE EBS1:DIBS1 RNA:DNA HYBRID 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 MOL_ID: 2; COMPND 7 MOLECULE: DNA_(5'-D(*CP*AP*GP*TP*GP*TP*C)-3')_; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: DIBS1; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 OTHER_DETAILS: IN VITRO TRANSCRIPTION FROM A SYNTHETIC DOUBLE- SOURCE 6 STRANDED DNA TEMPLATE USING T7 RNA POLYMERASE; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS RNA, DNA, RIBOZYME, GROUP II INTRON, HYBRID, REVERSE SPLICING, KEYWDS 2 RETROHOMING, DNA-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 18 AUTHOR M.SKILANDAT,R.K.O.SIGEL REVDAT 4 01-MAY-24 2M1V 1 REMARK REVDAT 3 06-AUG-14 2M1V 1 JRNL REVDAT 2 23-JUL-14 2M1V 1 JRNL REVDAT 1 11-JUN-14 2M1V 0 JRNL AUTH M.SKILANDAT,R.K.SIGEL JRNL TITL THE ROLE OF MG(II) IN DNA CLEAVAGE SITE RECOGNITION IN GROUP JRNL TITL 2 II INTRON RIBOZYMES: SOLUTION STRUCTURE AND METAL ION JRNL TITL 3 BINDING SITES OF THE RNADNA COMPLEX. JRNL REF J.BIOL.CHEM. V. 289 20650 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24895129 JRNL DOI 10.1074/JBC.M113.542381 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 3.0, X-PLOR NIH 2.3 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M1V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000103103. 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 : 0.6-0.9 MM RNA (29-MER), 0.7-1.0 REMARK 210 MM DNA (5'-D(*CP*AP*GP*TP*GP*TP* REMARK 210 C)-3'), 110 MM POTASSIUM REMARK 210 CHLORIDE, 10 UM EDTA, 100% D2O; REMARK 210 0.6-0.9 MM RNA (29-MER), 0.7-1.0 REMARK 210 MM DNA (5'-D(*CP*AP*GP*TP*GP*TP* REMARK 210 C)-3'), 110 MM POTASSIUM REMARK 210 CHLORIDE, 10 UM EDTA, 90% H2O/10% REMARK 210 D2O; 0.6-0.9 MM [U-100% 13C; U- REMARK 210 100% 15N] RNA (29-MER), 0.7-1.0 REMARK 210 MM DNA (5'-D(*CP*AP*GP*TP*GP*TP* REMARK 210 C)-3'), 110 MM POTASSIUM REMARK 210 CHLORIDE, 10 UM EDTA, 90% H2O/10% REMARK 210 D2O; 0.5-1.0 MM RNA (29-MER), REMARK 210 10 MM POTASSIUM CHLORIDE, 10 UM REMARK 210 EDTA, 100% D2O; 0.6-0.9 MM [3',4' REMARK 210 ,5',5'',5]-100% 2H RNA (29-MER), REMARK 210 0.7-1.0 MM DNA (5'-D(*CP*AP*GP* REMARK 210 TP*GP*TP*C)-3'), 110 MM REMARK 210 POTASSIUM CHLORIDE, 10 UM EDTA, REMARK 210 100% D2O; 0.6-0.9 MM [U-100% 13C; REMARK 210 U-100% 15N] RNA (29-MER), 0.7- REMARK 210 1.0 MM DNA (5'-D(*CP*AP*GP*TP*GP* REMARK 210 TP*C)-3'), 110 MM POTASSIUM REMARK 210 CHLORIDE, 10 UM EDTA, 100% D2O; REMARK 210 0.5-1.0 MM [U-100% 13C; U-100% REMARK 210 15N] RNA (29-MER), 10 MM REMARK 210 POTASSIUM CHLORIDE, 10 UM EDTA, REMARK 210 90% H2O/10% D2O; 0.5-1.0 MM RNA REMARK 210 (29-MER), 10 MM POTASSIUM REMARK 210 CHLORIDE, 10 UM EDTA, 90% H2O/10% REMARK 210 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 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 1D 31P; F1, F2 X- REMARK 210 FILTERED 1H-1H NOESY; F1, F2 X- REMARK 210 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 : TOPSPIN 3.0, SPARKY, DYANA 1.5, REMARK 210 CNS 1.2, X-PLOR NIH 2.3 REMARK 210 METHOD USED : MOLECULAR DYNAMICS, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18 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: 896 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6264 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 H2' C A 28 O4' C A 29 1.48 REMARK 500 O2' G A 1 H8 G A 2 1.55 REMARK 500 O2' U A 11 H5'' U A 12 1.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K65 RELATED DB: PDB REMARK 900 RELATED ID: 2K66 RELATED DB: PDB REMARK 900 RELATED ID: 18881 RELATED DB: BMRB REMARK 900 RELATED ID: 2M23 RELATED DB: PDB REMARK 900 RELATED ID: 2M24 RELATED DB: PDB DBREF 2M1V A 1 29 PDB 2M1V 2M1V 1 29 DBREF 2M1V B 59 65 PDB 2M1V 2M1V 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 DC DA DG DT DG DT DC 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