HEADER DNA 24-JUN-98 1BJD TITLE SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING SINGLE G*T TITLE 2 MISMATCHES USING RELAXATION MATRIX ANALYSIS AND RESTRAINED TITLE 3 MOLECULAR DYNAMICS, NMR, 1 STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*TP*GP*AP*CP*GP*TP*TP*AP*CP*G)- COMPND 3 3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DEOXYRIBONUCLEIC ACID, DNA, G*T MISMATCH, NMR EXPDTA SOLUTION NMR AUTHOR H.T.ALLAWI,J.SANTALUCIA JUNIOR REVDAT 4 24-FEB-09 1BJD 1 VERSN REVDAT 3 01-APR-03 1BJD 1 JRNL REVDAT 2 16-FEB-99 1BJD 3 ATOM COMPND REMARK TITLE REVDAT 2 2 3 SEQRES JRNL KEYWDS REVDAT 1 13-JAN-99 1BJD 0 JRNL AUTH H.T.ALLAWI,J.SANTALUCIA JR. JRNL TITL NMR SOLUTION STRUCTURE OF A DNA DODECAMER JRNL TITL 2 CONTAINING SINGLE G*T MISMATCHES. JRNL REF NUCLEIC ACIDS RES. V. 26 4925 1998 JRNL REFN ISSN 0305-1048 JRNL PMID 9776755 JRNL DOI 10.1093/NAR/26.21.4925 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED DISTANCES AND DIHEDRAL REMARK 3 ANGLES REMARK 4 REMARK 4 1BJD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : WATER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, COSY, HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR FELIX FELIX REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 13 REMARK 210 REMARK 210 REMARK: MEAN STRUCTURE. STRUCTURE WAS DETERMINED USING REMARK 210 RELAXATION MATRIX ANALYSIS OF NOE DATA. 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 DC A 1 C4' - C3' - C2' ANGL. DEV. = 6.1 DEGREES REMARK 500 DG A 2 C4' - C3' - C2' ANGL. DEV. = 5.6 DEGREES REMARK 500 DT A 3 C4' - C3' - C2' ANGL. DEV. = 5.5 DEGREES REMARK 500 DA A 5 C4' - C3' - C2' ANGL. DEV. = 5.8 DEGREES REMARK 500 DC A 6 C4' - C3' - C2' ANGL. DEV. = 5.8 DEGREES REMARK 500 DG A 7 C4' - C3' - C2' ANGL. DEV. = 5.8 DEGREES REMARK 500 DT A 8 C4' - C3' - C2' ANGL. DEV. = 5.6 DEGREES REMARK 500 DT A 9 C4' - C3' - C2' ANGL. DEV. = 5.8 DEGREES REMARK 500 DA A 10 C4' - C3' - C2' ANGL. DEV. = 5.6 DEGREES REMARK 500 DC A 11 C4' - C3' - C2' ANGL. DEV. = 5.5 DEGREES REMARK 500 DC B 1 C4' - C3' - C2' ANGL. DEV. = 6.1 DEGREES REMARK 500 DG B 2 C4' - C3' - C2' ANGL. DEV. = 5.6 DEGREES REMARK 500 DT B 3 C4' - C3' - C2' ANGL. DEV. = 5.5 DEGREES REMARK 500 DA B 5 C4' - C3' - C2' ANGL. DEV. = 5.7 DEGREES REMARK 500 DC B 6 C4' - C3' - C2' ANGL. DEV. = 5.8 DEGREES REMARK 500 DG B 7 C4' - C3' - C2' ANGL. DEV. = 5.7 DEGREES REMARK 500 DT B 8 C4' - C3' - C2' ANGL. DEV. = 5.6 DEGREES REMARK 500 DT B 9 C4' - C3' - C2' ANGL. DEV. = 5.7 DEGREES REMARK 500 DA B 10 C4' - C3' - C2' ANGL. DEV. = 5.6 DEGREES REMARK 500 DC B 11 C4' - C3' - C2' ANGL. DEV. = 5.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1BJD A 1 12 PDB 1BJD 1BJD 1 12 DBREF 1BJD B 1 12 PDB 1BJD 1BJD 1 12 SEQRES 1 A 12 DC DG DT DG DA DC DG DT DT DA DC DG SEQRES 1 B 12 DC DG DT DG DA DC DG DT DT DA DC DG 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 MASTER 84 0 0 0 0 0 0 6 0 0 0 2 END