1XHP - Header Asymmetric Unit

HEADER RNA 20-SEP-04 1XHP

TITLE SOLUTION STRUCTURE OF THE EXTENDED U6 ISL AS OBSERVED IN TITLE 2 THE U2/U6 COMPLEX FROM SACCHAROMYCES CEREVISIAE

COMPND MOL_ID: 1; COMPND 2 MOLECULE: U6 SNRNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: IN VITRO TRANSCRIPTION OF U6 NUCLEOTIDES 59- SOURCE 4 88 USING PURIFIED T7 RNA POLYMERASE AND SYNTHETIC DNA SOURCE 5 OLIGONUCLEOTIDES.

KEYWDS U6 RNA, RNA STEM-LOOP, PENTA-LOOP, INTERNAL BULGE, METAL KEYWDS 2 BINDING SITE

EXPDTA SOLUTION NMR

NUMMDL 10

AUTHOR D.G.SASHITAL,G.CORNILESCU,S.E.BUTCHER

REVDAT 3 24-FEB-09 1XHP 1 VERSN REVDAT 2 15-MAR-05 1XHP 1 JRNL REVDAT 1 23-NOV-04 1XHP 0

JRNL AUTH D.G.SASHITAL,G.CORNILESCU,C.J.MCMANUS,D.A.BROW, JRNL AUTH 2 S.E.BUTCHER JRNL TITL U2-U6 RNA FOLDING REVEALS A GROUP II INTRON-LIKE JRNL TITL 2 DOMAIN AND A FOUR-HELIX JUNCTION JRNL REF NAT.STRUCT.MOL.BIOL. V. 11 1237 2004 JRNL REFN ISSN 1545-9993 JRNL PMID 15543154 JRNL DOI 10.1038/NSMB863

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.9.7 REMARK 3 AUTHORS : C.D.SCHWIETERS,J.J.KUSZEWSKI,N.TJANDRA,G.M.CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 435 NOE DISTANCE CONSTRAINTS, 244 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 66 HYDROGEN BOND RESTRAINTS, 77 REMARK 3 RESIDUAL DIPOLAR COUPLINGS

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

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-SEP-04. REMARK 100 THE RCSB ID CODE IS RCSB030374.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 303; 298 REMARK 210 PH : 6.9; 7.5; 6.9 REMARK 210 IONIC STRENGTH : NULL; NULL; NULL REMARK 210 PRESSURE : NULL; NULL; NULL REMARK 210 SAMPLE CONTENTS : 1MM EXTENDED U6 ISL RNA; 90% REMARK 210 H2O; 10% D2O; 1MM EXTENDED U6 REMARK 210 ISL RNA; 99.99% D2O; 1MM 13C, REMARK 210 15N LABELED EXTENDED U6 ISL REMARK 210 RNA; 90% H2O; 10% D2O; 1MM REMARK 210 13C,15N LABELED EXTENDED U6 REMARK 210 ISL RNA; 99.99% D2O; 1MM 13C, REMARK 210 15N LABELED EXTENDED U6 ISL REMARK 210 RNA; 17 MG/ML PF1 REMARK 210 BACTERIOPHAGE; 90% H2O; 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, 3D_13C- REMARK 210 SEPARATED_NOESY, 3D [1H-13C- REMARK 210 1H] HCCH-TOCSY, 3D [1H-13C-1H] REMARK 210 HCCH -COSY, 2D [15N-1H] HNN- REMARK 210 COSY, J-MODULATED [13C-1H] CT- REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 750 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX, INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER, VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, VNMR 1.1, REMARK 210 NMRPIPE 97.027.12.56, SPARKY REMARK 210 3.105, CNS 1.1, XPLOR-NIH 2.9.7 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS, MOLECULAR REMARK 210 DYNAMICS, RESIDUAL DIPOLAR REMARK 210 COUPLINGS, CONFORMATIONAL REMARK 210 DATABASE POTENTIALS 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: 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: 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 O2' A A 2 O4' G A 3 2.08 REMARK 500 O2' A A 16 O5' U A 17 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 2 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 2 A A 2 C1' - O4' - C4' ANGL. DEV. = -4.6 DEGREES REMARK 500 3 A A 16 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 4 A A 2 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 5 A A 2 C1' - O4' - C4' ANGL. DEV. = -4.2 DEGREES REMARK 500 5 A A 5 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 6 A A 2 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 7 A A 2 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 8 A A 2 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 9 U A 17 C1' - O4' - C4' ANGL. DEV. = -8.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SY4 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE SHORTENED U6 ISL REMARK 900 RELATED ID: 1R2P RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF DOMAIN 5 FROM THE AI5(GAMMA) GROUP II REMARK 900 INTRON REMARK 900 RELATED ID: 1KXK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A RNA MOLECULE CONTAINING DOMAIN 5 AND REMARK 900 6 OF THE YEAST AI5G GROUP II SELF-SPLICING INTRON

DBREF 1XHP A 1 32 PDB 1XHP 1XHP 1 32

SEQRES 1 A 32 G A G C A G U U C C C C U SEQRES 2 A 32 G C A U A A G G A U G A A SEQRES 3 A 32 C C 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