10 20 30 40 50 60 70 80 1O15 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 21-OCT-02 1O15
TITLE THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, TITLE 2 REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE TITLE 3 AND BASE-BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR TITLE 4 COUPLINGS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: THEOPHYLLINE-BINDING RNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CONSENSUS SEQUENCE OF THE THEOPHYLLINE COMPND 6 BINDING RNA APTAMER FLANKED BY A FOUR BASE-PAIR STEM, A COMPND 7 THREE BASE-PAIR STEM, AND CAPPED BY A GAAA TETRALOOP
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS RIBONUCLEIC ACID, RNA
EXPDTA SOLUTION NMR
AUTHOR G.M.CLORE,J.KUSZEWSKI
REVDAT 2 24-FEB-09 1O15 1 VERSN REVDAT 1 18-FEB-03 1O15 0
JRNL AUTH G.M.CLORE,J.KUSZEWSKI JRNL TITL IMPROVING THE ACCURACY OF NMR STRUCTURES OF RNA BY JRNL TITL 2 MEANS OF CONFORMATIONAL DATABASE POTENTIALS OF JRNL TITL 3 MEAN FORCE AS ASSESSED BY COMPLETE DIPOLAR JRNL TITL 4 COUPLING CROSS-VALIDATION JRNL REF J.AM.CHEM.SOC. V. 125 1518 2003 JRNL REFN ISSN 0002-7863 JRNL PMID 12568611 JRNL DOI 10.1021/JA028383J
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.R.ZIMMERMANN,R.D.JENISON,C.L.WICK,J.P.SIMORRE, REMARK 1 AUTH 2 A.PARDI REMARK 1 TITL INTERLOCKING STRUCTURAL MOTIFS MEDIATE MOLECULAR REMARK 1 TITL 2 DISCRIMINATION BY A THEOPHYLLINE-BINDING RNA REMARK 1 REF NAT.STRUCT.BIOL. V. 4 644 1997 REMARK 1 REFN ISSN 1072-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH N.SIBILLE,A.PARDI,J.P.SIMORRE,M.BLACKLEDGE REMARK 1 TITL REFINEMENT OF LOCAL AND LONG RANGE STRUCTURAL REMARK 1 TITL 2 ORDER IN THEOPHYLLINE-BINDING RNA USING USING REMARK 1 TITL 3 13C-1H RESIDUAL DIPOLAR COUPLINGS AND RESTRAINED REMARK 1 TITL 4 MOLECULAR DYNAMICS. REMARK 1 REF J.AM.CHEM.SOC. V. 123 12135 2001 REMARK 1 REFN ISSN 0002-7863 REMARK 1 DOI 10.1021/JA011646+ REMARK 1 REFERENCE 3 REMARK 1 AUTH J.KUSZEWSKI,C.SCHWIETERS,G.M.CLORE REMARK 1 TITL IMPROVING THE ACCURACY OF NMR STRUCTURES OF DNA BY REMARK 1 TITL 2 MEANS OF A DATABASE POTENTIAL OF MEAN FORCE REMARK 1 TITL 3 DESCRIBING BASE-BASE POSITIONAL INTERACTIONS. REMARK 1 REF J.AM.CHEM.SOC. V. 123 3903 2001 REMARK 1 REFN ISSN 0002-7863 REMARK 1 DOI 10.1021/JA010033U
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH) REMARK 3 AUTHORS : CLORE, KUSZEWSKI, SCHWIETERS, TJANDRA REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF REMARK 3 223 NOE, 52 DISTANCES FOR WATSON-CRICK HYDROGEN BONDS, AND 110 REMARK 3 TORSION ANGLE RESTRAINTS, 101 CH DIPOLAR COUPLING RESTRAINTS. REMARK 3 THE EXPERIMENTAL RESTRAINTS ARE ESSENTIALLY THE SAME AS THOSE REMARK 3 LISTED IN N.SIBILLE,A.PARDI,J.P.SIMORRE,M.BLACKLEDGE REMARK 3 J.AM.CHEM.SOC. V 123, 12135 2001. THE NON-BONDED CONTACTS ARE REMARK 3 REPRESENTED BY A QUARTIC VAN DER WAALS REPULSION TERM, A BASE- REMARK 3 BASE POSITIONING DATABASE POTENTIAL OF MEAN FORCE, AND A REMARK 3 TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE.
REMARK 4 REMARK 4 1O15 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 8 REMARK 8 THE RESTRAINTS USED FOR DETERMINATION OF THIS STRUCTURE REMARK 8 ARE SUMMARIZED AS FOLLOWS: REMARK 8 REMARK 8 DISTANCE RESTRAINTS REMARK 8 30 INTRARESIDUE NOES REMARK 8 86 SEQUENTIAL NOES REMARK 8 17 MEDIUM RANGE (1 < |I-J|<5) NOES REMARK 8 90 LONG RANGE (|I-J|>=5) NOES REMARK 8 52 DISTANCES FOR 8 W-C BASE PAIRS AND 1 G-U REMARK 8 WOBBLE PAIR REMARK 8 TOTAL: 223 REMARK 8 REMARK 8 LOOSE TORSION ANGLE RESTRAINTS REMARK 8 31 DELTA REMARK 8 33 CHI REMARK 8 9 ALPHA, 9 BETA, 10 GAMMA, 9 EPSILON REMARK 8 AND 9 ZETA REMARK 8 TOTAL: 110. REMARK 8 REMARK 8 13C-1H DIPOLAR COUPLINGS REMARK 8 55 SUGAR REMARK 8 46 BASE REMARK 8 TOTAL 101
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-OCT-02. REMARK 100 THE RCSB ID CODE IS RCSB001672.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 250 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : RESTRAINED REGULARIZED MEAN REMARK 210 STRUCTURE REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE DIPOLAR COUPLINGS WERE DIVIDED INTO 10 PAIRS OF REMARK 210 WORKING AND TEST DATA SETS CHOSEN AT RANDOM AND PARTITIONED IN REMARK 210 A RATIO OF 70% (WORKING) AND 30% (TEST). 25 SIMULATED REMARK 210 ANNEALING STRUCTURES WERE CALCULATED FOR EACH PAIR, RESULTING REMARK 210 IN A TOTAL OF 250 STRUCTURES. THE STRUCTURE REPORTED HERE IS REMARK 210 OBTAINED BY RESTRAINED REGULARIZED OF THE MEAN COORDINATES OF REMARK 210 THE ENSEMBLE OF 250 INDIVIDUAL SIMULATED ANNEALING STRUCTURES REMARK 210 CALCULATED WITH COMPLETE DIPOLAR COUPLING CROSS-VALIDATION. REMARK 210 FOR THE ENSEMBLE OF 250 STRUCTURES THE WORKING DIPOLAR REMARK 210 COUPLING R-FACTOR IS 8.6+/-0.5% AND THE FREE DIPOLAR COUPLING REMARK 210 R-FACTOR IS 26.8+/-2.8%.
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 7 OP2 C A 8 2.04 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 C A 27 C6 - N1 - C2 ANGL. DEV. = 4.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TEP A 34
DBREF 1O15 A 1 33 PDB 1O15 1O15 1 33
SEQRES 1 A 33 G G C G A U A C C A G C C SEQRES 2 A 33 G A A A G G C C C U U G G SEQRES 3 A 33 C A G C G U C
HET TEP A 34 21
HETNAM TEP THEOPHYLLINE
FORMUL 2 TEP C7 H8 N4 O2
SITE 1 AC1 3 A A 7 C A 22 U A 24
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