10 20 30 40 50 60 70 80 2KF0 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 08-FEB-09 2KF0
TITLE NMR STRUCTURE OF U6 ISL AT PH 7.0
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*GP*GP*UP*UP*CP*CP*CP*CP*UP*GP*CP*AP*UP*AP*AP*GP*GP*AP*UP COMPND 4 *GP*AP*AP*CP*C)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS U6 RNA, STEM LOOP, BULGE, INTERNAL LOOP
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR V.VENDITTI,S.E.BUTCHER
REVDAT 2 01-SEP-09 2KF0 1 JRNL REVDAT 1 21-JUL-09 2KF0 0
JRNL AUTH V.VENDITTI,L.CLOS,N.NICCOLAI,S.E.BUTCHER JRNL TITL MINIMUM-ENERGY PATH FOR A U6 RNA CONFORMATIONAL JRNL TITL 2 CHANGE INVOLVING PROTONATION, BASE-PAIR JRNL TITL 3 REARRANGEMENT AND BASE FLIPPING. JRNL REF J.MOL.BIOL. V. 391 894 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19591840 JRNL DOI 10.1016/J.JMB.2009.07.003
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.J.REITER,L.J.NIKSTAD,A.M.ALLMANN,R.J.JOHNSON, REMARK 1 AUTH 2 S.E.BUTCHER REMARK 1 TITL STRUCTURE OF THE U6 RNA INTRAMOLECULAR STEM-LOOP REMARK 1 TITL 2 HARBORING AN S(P)-PHOSPHOROTHIOATE MODIFICATION. REMARK 1 REF RNA V. 9 533 2003 REMARK 1 REFN ISSN 1355-8382 REMARK 1 PMID 12702812 REMARK 1 REFERENCE 2 REMARK 1 AUTH N.J.REITER,H.BLAD,F.ABILDGAARD,S.E.BUTCHER REMARK 1 TITL DYNAMICS IN THE U6 RNA INTRAMOLECULAR STEM-LOOP: A REMARK 1 TITL 2 BASE FLIPPING CONFORMATIONAL CHANGE. REMARK 1 REF BIOCHEMISTRY V. 43 13739 2004 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 15504036 REMARK 1 DOI 10.1021/BI048815Y
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9.0 REMARK 3 AUTHORS : CASE, D. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2KF0 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-09. REMARK 100 THE RCSB ID CODE IS RCSB101039.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 283 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 50; 50 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM RNA, 100% D2O; 2 MM RNA, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, XWINNMR REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 12 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: 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 1 A A 14 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 G A 1 C5' - C4' - C3' ANGL. DEV. = -9.3 DEGREES REMARK 500 8 A A 12 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 9 G A 1 C5' - C4' - C3' ANGL. DEV. = -9.4 DEGREES REMARK 500 9 G A 2 O4' - C1' - N9 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 2 G A 16 0.07 SIDE_CHAIN REMARK 500 3 G A 16 0.07 SIDE_CHAIN REMARK 500 4 G A 16 0.07 SIDE_CHAIN REMARK 500 5 G A 16 0.07 SIDE_CHAIN REMARK 500 6 G A 16 0.06 SIDE_CHAIN REMARK 500 7 G A 16 0.07 SIDE_CHAIN REMARK 500 8 G A 16 0.07 SIDE_CHAIN REMARK 500 10 G A 16 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SY4 RELATED DB: PDB REMARK 900 U6 ISL STRUCTURE AT PH 7.0 REMARK 900 RELATED ID: 1SYZ RELATED DB: PDB REMARK 900 U6 ISL STRUCTURE AT PH 5.7 REMARK 900 RELATED ID: 2KEZ RELATED DB: PDB
DBREF 2KF0 A 1 24 PDB 2KF0 2KF0 1 24
SEQRES 1 A 24 G G U U C C C C U G C A U SEQRES 2 A 24 A A G G A U G A A C 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