HEADER RNA 25-JUN-04 1TUT TITLE J4/5 LOOP FROM THE CANDIDA ALBICANS AND CANDIDA TITLE 2 DUBLINIENSIS GROUP I INTRONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*AP*GP*GP*AP*AP*GP*GP*CP*GP*A)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-R(*UP*CP*GP*UP*UP*AP*AP*UP*CP*UP*C)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS RNA, NMR, INTERNAL LOOP, TANDEM MISMATCH, GU PAIRS, AA PAIRS EXPDTA SOLUTION NMR AUTHOR B.M.ZNOSKO,S.D.KENNEDY,P.C.WILLE,T.R.KRUGH,D.H.TURNER REVDAT 2 24-FEB-09 1TUT 1 VERSN REVDAT 1 28-DEC-04 1TUT 0 JRNL AUTH B.M.ZNOSKO,S.D.KENNEDY,P.C.WILLE,T.R.KRUGH, JRNL AUTH 2 D.H.TURNER JRNL TITL STRUCTURAL FEATURES AND THERMODYNAMICS OF THE J4/5 JRNL TITL 2 LOOP FROM THE CANDIDA ALBICANS AND CANDIDA JRNL TITL 3 DUBLINIENSIS GROUP I INTRONS. JRNL REF BIOCHEMISTRY V. 43 15822 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15595837 JRNL DOI 10.1021/BI049256Y REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 95.0 REMARK 3 AUTHORS : INSIGHT REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 217 NMR-DERIVED INTERPROTON DISTANCE RESTRAINTS (108 REMARK 3 INTRANUCLEOTIDE AND 109 INTERNUCLEOTIDE). HYDROGN BOND REMARK 3 RESTRAINTS WERE USED FOR THE SIX WC PAIRS AND FOR THE G8-U14 REMARK 3 WOBBLE PAIR. ON THE BASIS OF NMR DATA THAT IS CONSISTENT WITH REMARK 3 THE FORMATION OF TANDEM SHEARED AA PAIRS, TWO ARTIFICIAL REMARK 3 HYDROGEN BONDING RESTRAINTS WERE USED BETWEEN EACH SHEARED AA REMARK 3 PAIR. REMARK 4 REMARK 4 1TUT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-04. REMARK 100 THE RCSB ID CODE IS RCSB022919. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 6.1; 6.1 REMARK 210 IONIC STRENGTH : 80 MM NACL, 3 MM COBALT REMARK 210 HEXAMINE; 80 MM NACL, 3 MM REMARK 210 COBALT HEXAMINE REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : ~~2 MM RNA, 80 MM NACL, 3 MM REMARK 210 KH2PO4, 7 MM K2HPO4, 0.5 MM REMARK 210 NA2EDTA, 3 MM COBALT HEXAMINE, REMARK 210 PH=6.1, 90% H2O, 10% D2O; ~~2 REMARK 210 MM RNA, 80 MM NACL, 3 MM REMARK 210 KH2PO4, 7 MM K2HPO4, 0.5 MM REMARK 210 NA2EDTA, 3 MM COBALT HEXAMINE, REMARK 210 PH=6.1, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 5.2, FELIX 2000, REMARK 210 DISCOVER 95.0 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : CLOSEST TO AVERAGE 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 C A 9 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 G B 13 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 U B 14 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 U B 15 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 C B 19 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 U B 20 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES 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 A A 6 0.07 SIDE_CHAIN REMARK 500 G A 10 0.08 SIDE_CHAIN REMARK 500 U B 11B 0.09 SIDE_CHAIN REMARK 500 A B 16 0.07 SIDE_CHAIN REMARK 500 A B 17 0.06 SIDE_CHAIN REMARK 500 U B 18 0.08 SIDE_CHAIN REMARK 500 C B 19 0.07 SIDE_CHAIN REMARK 500 U B 20 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1TUT A 1 11 PDB 1TUT 1TUT 1 11 DBREF 1TUT B 11B 21 PDB 1TUT 1TUT 11 21 SEQRES 1 A 11 G A G G A A G G C G A SEQRES 1 B 11 U C G U U A A U C 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 MASTER 110 0 0 0 0 0 0 6 0 0 0 2 END