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 WITH T7 SOURCE 4 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 4 19-FEB-20 2JWV 1 REMARK 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 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, X-PLOR NIH REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CNS 1.1-SIMULATED ANNEALING FOLLOWED BY REMARK 3 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 12-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000100391. 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] RNA, REMARK 210 1 MM RNA, 90% H2O/10% D2O; 1 MM REMARK 210 RNA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-13C HSQC; 3D 1H-13C NOESY; REMARK 210 3D HCCH-TOCSY; 2D 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 : NULL 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 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 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' G A 14 H62 A A 16 1.56 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 9 C1' - O4' - C4' ANGL. DEV. = -4.2 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. = -5.0 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 113 0 0 0 0 0 0 6 0 0 0 3 END