HEADER DNA 22-JUN-99 1QSK TITLE NMR-DERIVED SOLUTION STRUCTURE OF A FIVE-ADENINE BULGE LOOP TITLE 2 WITHIN A DNA DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 D(GP*CP*AP*TP*CP*GP*AP*AP*AP*AP*AP*GP*CP*TP*AP*CP*GP)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*CP)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: ARTIFICIAL SEQUENCE; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: ARTIFICIAL SEQUENCE KEYWDS DNA BULGE, FIVE-ADENINE BULGE LOOP EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR U.DORNBERGER,A.HILLISCH,F.GOLLMICK,H.FRITZSCHE,S.DIEKMANN REVDAT 3 24-FEB-09 1QSK 1 VERSN REVDAT 2 01-APR-03 1QSK 1 JRNL REVDAT 1 05-NOV-99 1QSK 0 JRNL AUTH U.DORNBERGER,A.HILLISCH,F.A.GOLLMICK,H.FRITZSCHE, JRNL AUTH 2 S.DIEKMANN JRNL TITL SOLUTION STRUCTURE OF A FIVE-ADENINE BULGE LOOP JRNL TITL 2 WITHIN A DNA DUPLEX. JRNL REF BIOCHEMISTRY V. 38 12860 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10504256 JRNL DOI 10.1021/BI9906874 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 5.0 REMARK 3 AUTHORS : PEARLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QSK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUN-99. REMARK 100 THE RCSB ID CODE IS RCSB009214. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300; 278 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 100MM NACL; 100MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2.8MM IN DUPLEX; 10MM REMARK 210 PHOSPHATE BUFFER, 100MM NACL, REMARK 210 0.05MM EDTA, 100% D2O; 2.8MM REMARK 210 IN DUPLEX; 10MM PHOSPHATE REMARK 210 BUFFER, 100MM NACL, 0.05MM REMARK 210 EDTA, 90% H2O,10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY, E-COSY, P REMARK 210 -COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 4.3, NMRPIPE 1.7, REMARK 210 MARDIGRAS 3.2, DYANA 1.5, REMARK 210 AMBER 5.0 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS AND REMARK 210 RESTRAINED ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 600 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 6 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DA A 9 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DA B 21 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DC B 23 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT B 27 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC B 29 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DT B 20 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA B 21 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC B 23 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DT B 27 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DC B 29 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 DC A 2 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DC B 18 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 DA B 21 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DC B 23 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DC B 24 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DT B 27 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DC B 29 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 4 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 4 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 4 DA A 10 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DG A 12 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 DC B 18 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DA B 21 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 4 DC B 23 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 4 DT B 27 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 4 DC B 29 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 DC A 2 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 5 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 5 DG A 12 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 5 DC A 16 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 5 DC B 23 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 5 DT B 27 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 5 DC B 29 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 6 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 6 DA A 9 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 DA A 10 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 6 DG A 12 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 129 ANGLE DEVIATIONS. 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 DT A 4 0.08 SIDE_CHAIN REMARK 500 1 DC A 5 0.06 SIDE_CHAIN REMARK 500 1 DA A 8 0.07 SIDE_CHAIN REMARK 500 1 DG B 19 0.07 SIDE_CHAIN REMARK 500 1 DC B 24 0.09 SIDE_CHAIN REMARK 500 1 DG B 25 0.07 SIDE_CHAIN REMARK 500 2 DT A 4 0.09 SIDE_CHAIN REMARK 500 2 DA A 8 0.07 SIDE_CHAIN REMARK 500 2 DG A 12 0.07 SIDE_CHAIN REMARK 500 2 DG B 19 0.08 SIDE_CHAIN REMARK 500 2 DC B 24 0.10 SIDE_CHAIN REMARK 500 2 DG B 25 0.07 SIDE_CHAIN REMARK 500 3 DA A 8 0.06 SIDE_CHAIN REMARK 500 3 DA A 9 0.05 SIDE_CHAIN REMARK 500 3 DG A 12 0.07 SIDE_CHAIN REMARK 500 3 DG B 19 0.10 SIDE_CHAIN REMARK 500 3 DC B 24 0.07 SIDE_CHAIN REMARK 500 3 DG B 25 0.07 SIDE_CHAIN REMARK 500 3 DT B 27 0.07 SIDE_CHAIN REMARK 500 4 DT A 4 0.08 SIDE_CHAIN REMARK 500 4 DA A 8 0.08 SIDE_CHAIN REMARK 500 4 DG A 12 0.07 SIDE_CHAIN REMARK 500 4 DG B 19 0.09 SIDE_CHAIN REMARK 500 4 DC B 24 0.12 SIDE_CHAIN REMARK 500 4 DG B 25 0.07 SIDE_CHAIN REMARK 500 4 DT B 27 0.06 SIDE_CHAIN REMARK 500 5 DA A 3 0.06 SIDE_CHAIN REMARK 500 5 DT A 4 0.10 SIDE_CHAIN REMARK 500 5 DA A 8 0.06 SIDE_CHAIN REMARK 500 5 DG A 12 0.07 SIDE_CHAIN REMARK 500 5 DG B 19 0.07 SIDE_CHAIN REMARK 500 5 DC B 24 0.09 SIDE_CHAIN REMARK 500 5 DG B 25 0.05 SIDE_CHAIN REMARK 500 6 DA A 3 0.05 SIDE_CHAIN REMARK 500 6 DT A 4 0.08 SIDE_CHAIN REMARK 500 6 DA A 8 0.07 SIDE_CHAIN REMARK 500 6 DG A 17 0.06 SIDE_CHAIN REMARK 500 6 DC B 18 0.07 SIDE_CHAIN REMARK 500 6 DG B 19 0.07 SIDE_CHAIN REMARK 500 6 DC B 24 0.07 SIDE_CHAIN REMARK 500 6 DG B 25 0.07 SIDE_CHAIN REMARK 500 7 DT A 4 0.08 SIDE_CHAIN REMARK 500 7 DC A 5 0.06 SIDE_CHAIN REMARK 500 7 DA A 8 0.08 SIDE_CHAIN REMARK 500 7 DG A 12 0.07 SIDE_CHAIN REMARK 500 7 DG B 19 0.09 SIDE_CHAIN REMARK 500 7 DG B 22 0.05 SIDE_CHAIN REMARK 500 7 DC B 24 0.12 SIDE_CHAIN REMARK 500 7 DG B 25 0.08 SIDE_CHAIN REMARK 500 7 DA B 26 0.05 SIDE_CHAIN REMARK 500 8 DA A 3 0.05 SIDE_CHAIN REMARK 500 8 DT A 4 0.08 SIDE_CHAIN REMARK 500 8 DA A 8 0.06 SIDE_CHAIN REMARK 500 8 DG A 12 0.07 SIDE_CHAIN REMARK 500 8 DG B 19 0.08 SIDE_CHAIN REMARK 500 8 DG B 25 0.07 SIDE_CHAIN REMARK 500 9 DT A 4 0.08 SIDE_CHAIN REMARK 500 9 DA A 8 0.07 SIDE_CHAIN REMARK 500 9 DG A 12 0.07 SIDE_CHAIN REMARK 500 9 DG B 19 0.10 SIDE_CHAIN REMARK 500 9 DC B 24 0.09 SIDE_CHAIN REMARK 500 9 DG B 25 0.08 SIDE_CHAIN REMARK 500 10 DA A 3 0.06 SIDE_CHAIN REMARK 500 10 DT A 4 0.08 SIDE_CHAIN REMARK 500 10 DA A 8 0.06 SIDE_CHAIN REMARK 500 10 DG A 12 0.07 SIDE_CHAIN REMARK 500 10 DG B 19 0.07 SIDE_CHAIN REMARK 500 10 DC B 24 0.13 SIDE_CHAIN REMARK 500 10 DG B 25 0.06 SIDE_CHAIN REMARK 500 11 DT A 4 0.07 SIDE_CHAIN REMARK 500 11 DG A 6 0.05 SIDE_CHAIN REMARK 500 11 DA A 7 0.05 SIDE_CHAIN REMARK 500 11 DA A 8 0.06 SIDE_CHAIN REMARK 500 11 DG A 12 0.07 SIDE_CHAIN REMARK 500 11 DC B 24 0.08 SIDE_CHAIN REMARK 500 11 DG B 25 0.08 SIDE_CHAIN REMARK 500 11 DT B 27 0.06 SIDE_CHAIN REMARK 500 12 DT A 4 0.07 SIDE_CHAIN REMARK 500 12 DG A 6 0.05 SIDE_CHAIN REMARK 500 12 DA A 7 0.05 SIDE_CHAIN REMARK 500 12 DA A 8 0.06 SIDE_CHAIN REMARK 500 12 DG A 12 0.06 SIDE_CHAIN REMARK 500 12 DG B 19 0.08 SIDE_CHAIN REMARK 500 12 DC B 24 0.10 SIDE_CHAIN REMARK 500 12 DG B 25 0.09 SIDE_CHAIN REMARK 500 13 DA A 3 0.05 SIDE_CHAIN REMARK 500 13 DT A 4 0.08 SIDE_CHAIN REMARK 500 13 DA A 8 0.07 SIDE_CHAIN REMARK 500 13 DA A 11 0.05 SIDE_CHAIN REMARK 500 13 DG A 12 0.05 SIDE_CHAIN REMARK 500 13 DG B 19 0.08 SIDE_CHAIN REMARK 500 13 DG B 22 0.05 SIDE_CHAIN REMARK 500 13 DC B 24 0.10 SIDE_CHAIN REMARK 500 13 DG B 25 0.08 SIDE_CHAIN REMARK 500 14 DT A 4 0.07 SIDE_CHAIN REMARK 500 14 DA A 8 0.06 SIDE_CHAIN REMARK 500 14 DG A 12 0.06 SIDE_CHAIN REMARK 500 14 DG B 25 0.06 SIDE_CHAIN REMARK 500 14 DT B 27 0.07 SIDE_CHAIN REMARK 500 15 DT A 4 0.07 SIDE_CHAIN REMARK 500 15 DC A 5 0.06 SIDE_CHAIN REMARK 500 15 DA A 7 0.06 SIDE_CHAIN REMARK 500 15 DA A 8 0.06 SIDE_CHAIN REMARK 500 15 DC A 13 0.07 SIDE_CHAIN REMARK 500 15 DG B 19 0.08 SIDE_CHAIN REMARK 500 15 DC B 24 0.07 SIDE_CHAIN REMARK 500 15 DG B 25 0.07 SIDE_CHAIN REMARK 500 15 DT B 27 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AJT RELATED DB: PDB REMARK 900 FIVE-NUCLEOTIDE RNA BULGE DBREF 1QSK A 1 17 PDB 1QSK 1QSK 1 17 DBREF 1QSK B 18 29 PDB 1QSK 1QSK 18 29 SEQRES 1 A 17 DG DC DA DT DC DG DA DA DA DA DA DG DC SEQRES 2 A 17 DT DA DC DG SEQRES 1 B 12 DC DG DT DA DG DC DC DG DA DT DG DC 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 252 0 0 0 0 0 0 6 0 0 0 3 END