Header list of 1o15.pdb file
Complete list - 23 20 Bytes
HEADER RNA 21-OCT-02 1O15 TITLE THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, TITLE 2 REGULARIZED MEAN STRUCTURE, REFINEMENT WITH TORSION ANGLE AND BASE- TITLE 3 BASE POSITIONAL DATABASE POTENTIALS AND DIPOLAR 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 BINDING RNA COMPND 6 APTAMER FLANKED BY A FOUR BASE-PAIR STEM, A THREE BASE-PAIR STEM, AND COMPND 7 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 3 23-FEB-22 1O15 1 REMARK 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 MEANS OF JRNL TITL 2 CONFORMATIONAL DATABASE POTENTIALS OF MEAN FORCE AS ASSESSED JRNL TITL 3 BY COMPLETE DIPOLAR 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,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 ORDER IN REMARK 1 TITL 2 THEOPHYLLINE-BINDING RNA USING USING 13C-1H RESIDUAL DIPOLAR REMARK 1 TITL 3 COUPLINGS AND RESTRAINED 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 MEANS OF REMARK 1 TITL 2 A DATABASE POTENTIAL OF MEAN FORCE DESCRIBING BASE-BASE REMARK 1 TITL 3 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 TORSION REMARK 3 ANGLE DATABASE POTENTIAL OF MEAN FORCE. REMARK 4 REMARK 4 1O15 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 8 REMARK 8 THE RESTRAINTS USED FOR DETERMINATION OF THIS STRUCTURE REMARK 8 ARE SUMMARIZED AS FOLLOWS: 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 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 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 DEPOSITION ID IS D_1000001672. 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 REMARK 210 OF WORKING AND TEST DATA SETS CHOSEN AT RANDOM AND REMARK 210 PARTITIONED IN A RATIO OF 70% (WORKING) AND REMARK 210 30% (TEST). 25 SIMULATED ANNEALING STRUCTURES REMARK 210 WERE CALCULATED FOR EACH PAIR, RESULTING IN A TOTAL REMARK 210 OF 250 STRUCTURES. THE STRUCTURE REPORTED HERE IS REMARK 210 OBTAINED BY RESTRAINED REGULARIZED OF THE MEAN REMARK 210 COORDINATES OF THE ENSEMBLE OF 250 INDIVIDUAL REMARK 210 SIMULATED ANNEALING STRUCTURES CALCULATED WITH REMARK 210 COMPLETE DIPOLAR COUPLING CROSS-VALIDATION. REMARK 210 FOR THE ENSEMBLE OF 250 STRUCTURES THE WORKING REMARK 210 DIPOLAR COUPLING R-FACTOR IS 8.6+/-0.5% AND REMARK 210 THE FREE DIPOLAR COUPLING 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 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: 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
Complete list - 23 20 Bytes