HEADER RNA 29-SEP-03 1R2P TITLE SOLUTION STRUCTURE OF DOMAIN 5 FROM THE AI5(GAMMA) GROUP II INTRON COMPND MOL_ID: 1; COMPND 2 MOLECULE: 34-MER; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOMAIN 5 OF THE AI5(GAMMA) GROUP II INTRON; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE OCCURS NATURALLY IN SACCHAROMYCES CEREVISIAE SOURCE 4 (BAKER'S YEAST) AND WAS SYNTHESIZED IN VITRO USING T7 RNA POLYMERASE SOURCE 5 AND SYNTHETIC DNA OLIGONUCLEOTIDES. KEYWDS RNA HAIRPIN, TETRALOOP, BULGE, METAL ION, MAGNESIUM, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR R.K.O.SIGEL,D.G.SASHITAL,D.L.ABRAMOVITZ,A.G.PALMER III,S.E.BUTCHER, AUTHOR 2 A.M.PYLE REVDAT 3 02-MAR-22 1R2P 1 REMARK REVDAT 2 24-FEB-09 1R2P 1 VERSN REVDAT 1 03-FEB-04 1R2P 0 JRNL AUTH R.K.SIGEL,D.G.SASHITAL,D.L.ABRAMOVITZ,A.G.PALMER, JRNL AUTH 2 S.E.BUTCHER,A.M.PYLE JRNL TITL SOLUTION STRUCTURE OF DOMAIN 5 OF A GROUP II INTRON RIBOZYME JRNL TITL 2 REVEALS A NEW RNA MOTIF. JRNL REF NAT.STRUCT.MOL.BIOL. V. 11 187 2004 JRNL REFN ISSN 1545-9993 JRNL PMID 14745440 JRNL DOI 10.1038/NSMB717 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, CNS 1.1 REMARK 3 AUTHORS : BRUNGER ET. AL. (CNS), BRUNGER ET. AL. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES BASED ON 678 NOE-DERIVED REMARK 3 DISTANCE RESTRAINTS, 261 DIHEDRAL RESTRAINTS, 72 HYDROGEN BOND REMARK 3 RESTRAINTS, AND 24 RESIDUAL DIPOLAR COUPLING RESTRAINTS REMARK 4 REMARK 4 1R2P COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020362. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 298; 308; 291; 303 REMARK 210 PH : 6.5; 6.5; 6.5; 6.5; 6.5 REMARK 210 IONIC STRENGTH : 100MM KCL; 100MM KCL; 100MM KCL; REMARK 210 100MM KCL; 100MM KCL REMARK 210 PRESSURE : NULL; NULL; NULL; NULL; NULL REMARK 210 SAMPLE CONTENTS : 0.5 - 0.7 MM D5 RNA; 0 - 200MM REMARK 210 KCL, 0 - 20 MM MGCL2, 0.01 MM REMARK 210 EDTA, 90% H2O, 10% D2O; 0.5 - REMARK 210 0.7 MM D5 RNA; 0 - 200MM KCL, 0 - REMARK 210 20 MM MGCL2, 0.01 MM EDTA, REMARK 210 99.999% D2O; 0.5 - 0.7 MM D5 RNA, REMARK 210 13C-15N LABELED; 100MM KCL, REMARK 210 0.01 MM EDTA, 90% H2O, 10% D2O; REMARK 210 0.5 - 0.7 MM D5 RNA, 13C-15N REMARK 210 LABELED; 100MM KCL, 0.01 MM EDTA, REMARK 210 99.999% D2O; 0.5 - 0.7 MM D5 REMARK 210 RNA, 13C-15N LABELED; 100MM KCL, REMARK 210 0.01 MM EDTA, 17 MG/ML PF1 REMARK 210 FILAMENTOUS BACTERIOPHAGE, 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 3D 1H-13C-1H REMARK 210 HCCH TOCSY; 3D 1H-13C-1H HCCH REMARK 210 COSY; 2D 2JHN HNN-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA, SPARKY 3, XWINNMR 2.6 REMARK 210 METHOD USED : TORSION ANGLE MOLECULAR DYNAMICS REMARK 210 CARTESIAN SPACE SIMULATED REMARK 210 ANNEALING AND MOLECULAR DYNAMICS REMARK 210 RESIDUAL DIPOLAR COUPLINGS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: RESIDUAL DIPOLAR COUPLINGS WERE MEASURED USING 1H-13C HSQC REMARK 210 COUPLED IN EITHER THE PROTON OR THE CARBON DIMENSION 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 8 G A 15 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5962 RELATED DB: BMRB REMARK 900 NMR DATA: CHEMICAL SHIFTS OF DOMAIN 5 REMARK 900 RELATED ID: 1KXK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A DOMAIN5 / DOMAIN 6 CONSTRUCT FROM AI5GAMMA DBREF 1R2P A 1 34 PDB 1R2P 1R2P 1 34 SEQRES 1 A 34 G A G C C G U A U G C G A SEQRES 2 A 34 U G A A A G U C G C A C G SEQRES 3 A 34 U A C G G U 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 MODEL 1