1SY4 - Header Asymmetric Unit

HEADER RNA 31-MAR-04 1SY4

TITLE REFINED SOLUTION STRUCTURE OF THE S. CEREVISIAE U6 TITLE 2 INTRAMOLECULAR STEM LOOP (ISL) RNA USING RESIDUAL DIPOLAR TITLE 3 COUPLINGS (RDCS)

COMPND MOL_ID: 1; COMPND 2 MOLECULE: U6 INTRAMOLECULAR STEM-LOOP RNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: MUTATION A62G

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: IN VITRO T7 RNA POLYMERASE TRANSCRIPTION

KEYWDS RNA, STEM-LOOP (GNRA-LIKE TETRALOOP), A-C WOBBLE PAIR, KEYWDS 2 INTERNAL LOOP

EXPDTA SOLUTION NMR

NUMMDL 12

AUTHOR N.J.REITER,L.J.NIKSTAD,A.M.ALLMAN,R.J.JOHNSON,S.E.BUTCHER

REVDAT 2 24-FEB-09 1SY4 1 VERSN REVDAT 1 06-APR-04 1SY4 0

SPRSDE 06-APR-04 1SY4 1NYZ

JRNL AUTH N.J.REITER,L.J.NIKSTAD,A.M.ALLMAN,R.J.JOHNSON, JRNL AUTH 2 S.E.BUTCHER JRNL TITL STRUCTURE OF THE U6 RNA INTRAMOLECULAR STEM-LOOP JRNL TITL 2 HARBORING AN S(P)-PHOSPHOROTHIOATE MODIFICATION. JRNL REF RNA V. 9 533 2003 JRNL REFN ISSN 1355-8382 JRNL PMID 12702812 JRNL DOI 10.1261/RNA.2199103

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.HUPPLER,L.J.NIKSTAD,A.M.ALLMANN,D.A.BROW, REMARK 1 AUTH 2 S.E.BUTCHER REMARK 1 TITL METAL BINDING AND BASE IONIZATION IN THE U6 RNA REMARK 1 TITL 2 INTRAMOLECULAR STEM-LOOP STRUCTURE REMARK 1 REF NAT.STRUCT.BIOL. V. 9 431 2002 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 11992125 REMARK 1 DOI 10.1038/NSB800

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLORNIH 2.0.6. REMARK 3 AUTHORS : CLORE, G.M. ET. AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1SY4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-APR-04. REMARK 100 THE RCSB ID CODE IS RCSB022085.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 285 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 50 MM NACL; 50 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8-1.4 MM RNA, 50 MM NACL, REMARK 210 PH 7.0; 0.8-1.4 MM RNA, 50 MM REMARK 210 NACL, PH 7.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, 2D 1H-13C REMARK 210 HSQC 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 : CNS 1.1, XWINNMR 2.6, SPARKY REMARK 210 3.0 REMARK 210 METHOD USED : XPLOR-NIH 2.0.6 STRUCTURE REMARK 210 CALCULATION WHICH INCORPORATES REMARK 210 RESIDUAL DIPOLAR COUPLINGS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 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: T7 RNA TRANSCRIPT FROM SYNTHETIC DNA (SEQUENCE FROM REMARK 210 SACCHAROMYCES CEREVISIAE)

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 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 17 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 18 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 20 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 20 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 21 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 22 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 17 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 18 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 20 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 20 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 21 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A A 22 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 3 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 17 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 A A 18 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 218 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LC6 RELATED DB: PDB REMARK 900 U6 ISL RNA PH 7.0 (WITHOUT RDCS) REMARK 900 RELATED ID: 1NZ1 RELATED DB: PDB REMARK 900 U6 ISL RNA SP-PHOSPHOROTHIOATE SUBSTITUTED U80 (WITH RDCS) REMARK 900 RELATED ID: 1NC0 RELATED DB: PDB REMARK 900 U6 ISL RNA U80G REMARK 900 RELATED ID: 1SYZ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE S. CEREVISIAE U6 INTRAMOLECULAR REMARK 900 STEM-LOOP (ISL) RNA AT PH 5.7

DBREF 1SY4 A 1 24 PDB 1SY4 1SY4 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