2JWV - Header Asymmetric Unit

HEADER RNA 25-OCT-07 2JWV

TITLE STRUCTURE OF A HIGH AFFINITY ANTI-NFKB RNA APTAMER

COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (29-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION SOURCE 4 WITH T7 RNA POLYMERASE

KEYWDS RNA, ASYMMETRIC INTERNAL BULGE, STEM LOOP

EXPDTA SOLUTION NMR

NUMMDL 10

AUTHOR N.J.REITER,L.MAHER III,S.E.BUTCHER

REVDAT 3 24-FEB-09 2JWV 1 VERSN REVDAT 2 11-MAR-08 2JWV 1 JRNL REVDAT 1 08-JAN-08 2JWV 0

JRNL AUTH N.J.REITER,L.J.MAHER,S.E.BUTCHER JRNL TITL DNA MIMICRY BY A HIGH-AFFINITY ANTI-NF-KAPPAB RNA JRNL TITL 2 APTAMER JRNL REF NUCLEIC ACIDS RES. V. 36 1227 2008 JRNL REFN ISSN 0305-1048 JRNL PMID 18160411 JRNL DOI 10.1093/NAR/GKM1141

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CNS 1.1-SIMULATED ANNEALING FOLLOWED REMARK 3 BY A XPLOR-NIH REFINEMENT PROTOCOL

REMARK 4 REMARK 4 2JWV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-07. REMARK 100 THE RCSB ID CODE IS RCSB100391.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 13C; U-99% 15N] REMARK 210 RNA, 1 MM RNA, 90% H2O/10% REMARK 210 D2O; 1 MM RNA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY, 2D 1H-1H REMARK 210 TOCSY, 2D 1H-13C HSQC, 3D 1H- REMARK 210 13C NOESY, 3D HCCH-TOCSY, 2D REMARK 210 1H-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ, 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA, DMX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN, BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 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 9 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 2 A A 9 C1' - O4' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 4 A A 9 C1' - O4' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 5 A A 9 C1' - O4' - C4' ANGL. DEV. = -5.3 DEGREES REMARK 500 6 A A 9 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 7 A A 9 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 8 A A 9 C1' - O4' - C4' ANGL. DEV. = -4.7 DEGREES REMARK 500 9 A A 9 C1' - O4' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 10 A A 9 C1' - O4' - C4' ANGL. DEV. = -5.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OOA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NF-KB (P50)2 BOUND TO RNA REMARK 900 RELATED ID: 15538 RELATED DB: BMRB

DBREF 2JWV A 1 29 PDB 2JWV 2JWV 1 29

SEQRES 1 A 29 G A U A C U U G A A A C U SEQRES 2 A 29 G U A A G G U U G G C G U SEQRES 3 A 29 A 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