2RPT - Header Asymmetric Unit

HEADER RNA 23-AUG-08 2RPT

TITLE STRUCTURE OF THE CC MISMATCH FROM THE THYMIDYLATE SYNTHASE TITLE 2 BINDING SITE 1 HAIRPIN AND ANALYSIS OF ITS INTERACTION WITH TITLE 3 PAROMOMYCIN

COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*GP*GP*CP*CP*CP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*CP*GP*GP*CP COMPND 4 *C)-3'); COMPND 5 CHAIN: A; COMPND 6 FRAGMENT: THYMIDYLATE SYNTHASE BINDING SITE 1 MRNA HAIRPIN; COMPND 7 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: IN-VITRO TRANSCRIPTION USING T7 RNA SOURCE 4 POLYMERASE

KEYWDS NMR SPECTROSCOPY, RNA STRUCTURE, PAROMOMYCIN, KEYWDS 2 AMINOGLYCOSIDE-RNA INTERACTION

EXPDTA SOLUTION NMR

NUMMDL 10

AUTHOR T.J.TAVARES,P.E.JOHNSON

REVDAT 1 25-AUG-09 2RPT 0

JRNL AUTH T.J.TAVARES,A.V.BERIBISKY,P.E.JOHNSON JRNL TITL STRUCTURE OF THE CYTOSINE-CYTOSINE MISMATCH IN THE JRNL TITL 2 THYMIDYLATE SYNTHASE MRNA BINDING SITE AND ANALYSIS JRNL TITL 3 OF ITS INTERACTION WITH THE AMINOGLYCOSIDE JRNL TITL 4 PAROMOMYCIN JRNL REF RNA V. 15 911 2009 JRNL REFN ISSN 1355-8382 JRNL PMID 19329536 JRNL DOI 10.1261/RNA.1514909

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH 2.19 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 2RPT COMPLIES WITH FORMAT V. 3.20, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-AUG-08. REMARK 100 THE RCSB ID CODE IS RCSB150139.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 293 REMARK 210 PH : NULL; NULL REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : NULL; NULL REMARK 210 SAMPLE CONTENTS : 3-5 MG/ML RNA, 90% H2O/10% REMARK 210 D2O AND 100% D2O; 3-5 MG/ML [U REMARK 210 -100% 13C; U-100% 15N] RNA, REMARK 210 90% H2O/10% D2O AND 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H REMARK 210 TOCSY; 2D 1H-1H COSY; 2D 1H- REMARK 210 13C HSQC; 3D 1H-13C NOESY- REMARK 210 HSQC; 3D HCCH-COSY; 3D HCCH- REMARK 210 TOCSY; 2D 1H-15N HSQC; 3D 1H- REMARK 210 15N NOESY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, NMRPIPE, NMRDRAW, REMARK 210 NMRVIEW REMARK 210 METHOD USED : SIMULATED ANNEALING, REMARK 210 MOLECULAR DYNAMICS 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 9 C A 5 C1' - O4' - C4' ANGL. DEV. = -4.5 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 1 C A 8 0.06 SIDE_CHAIN REMARK 500 2 C A 8 0.06 SIDE_CHAIN REMARK 500 3 C A 8 0.08 SIDE_CHAIN REMARK 500 5 C A 8 0.07 SIDE_CHAIN REMARK 500 6 C A 8 0.06 SIDE_CHAIN REMARK 500 7 C A 3 0.06 SIDE_CHAIN REMARK 500 8 C A 8 0.07 SIDE_CHAIN REMARK 500 9 G A 13 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL

DBREF 2RPT A 1 20 PDB 2RPT 2RPT 1 20

SEQRES 1 A 20 G G C C C G C C G A A A G SEQRES 2 A 20 G C C G G 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