HEADER DNA 15-AUG-01 1JRV TITLE SOLUTION STRUCTURE OF DAATAA DNA BULGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 D(*GP*CP*AP*TP*CP*GP*AP*AP*TP*AP*AP*GP*CP*TP*AP*CP*G)-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*C)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DNA BULGE, FIVE-NUCLEOTIDE BULGE LOOP, DEOXYRIBONUCLEIC ACID EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR F.A.GOLLMICK,M.LORENZ,U.DORNBERGER,J.VON LANGEN,S.DIEKMANN, AUTHOR 2 H.FRITZSCHE REVDAT 2 24-FEB-09 1JRV 1 VERSN REVDAT 1 19-JUN-02 1JRV 0 JRNL AUTH F.A.GOLLMICK,M.LORENZ,U.DORNBERGER,J.VON LANGEN, JRNL AUTH 2 S.DIEKMANN,H.FRITZSCHE JRNL TITL SOLUTION STRUCTURE OF DAATAA AND DAAUAA DNA BULGES. JRNL REF NUCLEIC ACIDS RES. V. 30 2669 2002 JRNL REFN ISSN 0305-1048 JRNL PMID 12060684 JRNL DOI 10.1093/NAR/GKF375 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 5.0 REMARK 3 AUTHORS : WEINER, S.J., KOLLMAN, P.A., NGUYEN, D.T., REMARK 3 CASE, D.A. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 906 RESTRAINTS, 645 ARE NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 235 DIHEDRAL ANGLE RESTRAINTS, 26 DISTANCE RESTRAINTS FROM REMARK 3 HYDROGEN BONDS. REMARK 4 REMARK 4 1JRV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-AUG-01. REMARK 100 THE RCSB ID CODE IS RCSB014116. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300; 278 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : 100MM NA+; 100MM NA+ REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.6MM IN DUPLEX; 10MM REMARK 210 PHOSPHATE BUFFER; 100MM NACL; REMARK 210 0.05MM EDTA; 100% D2O; 1.6MM REMARK 210 IN DUPLEX; 10MM PHOSPHATE REMARK 210 BUFFER; 100MM NACL; 0.05MM REMARK 210 EDTA; 90% H2O, 10% D2O; 1.6MM REMARK 210 IN DUPLEX; 100MM NACL; 0.05MM REMARK 210 EDTA; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D_NOESY, E-COSY, 31P-1H_ REMARK 210 CORRELATED REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 500 MHZ, 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 3, MARDIGRAS 3.2, REMARK 210 DYANA 1.5, CURVES 4.0, AMBER REMARK 210 5.0 REMARK 210 METHOD USED : MATRIX RELAXATION (MARDIGRAS) REMARK 210 ; TORSION ANGLE DYNAMICS REMARK 210 (DYANA); ENERGY MINIMIZATION REMARK 210 (AMBER) REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR AND HETERONUCLEAR 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. = 3.1 DEGREES REMARK 500 1 DA A 3 O4' - C4' - C3' ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DA A 11 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 13 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC A 16 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT B 20 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT B 27 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DC B 29 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DA A 3 O4' - C4' - C3' ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DA A 7 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT A 9 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA A 10 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 2 DA A 11 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DC A 13 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DC A 16 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DC B 18 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DT B 20 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DA B 26 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DT B 27 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DC B 29 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DA A 3 O4' - C4' - C3' ANGL. DEV. = 5.8 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 3 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DA A 7 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 DA A 10 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 3 DA A 11 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 3 DC A 13 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DA A 15 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 3 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DT B 20 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DA B 26 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 3 DC B 29 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 4 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 4 DA A 3 O4' - C4' - C3' ANGL. DEV. = 5.0 DEGREES REMARK 500 4 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 4 DT A 4 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES REMARK 500 4 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 218 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 DA A 3 0.12 SIDE_CHAIN REMARK 500 1 DT A 4 0.09 SIDE_CHAIN REMARK 500 1 DC A 13 0.08 SIDE_CHAIN REMARK 500 1 DG B 19 0.07 SIDE_CHAIN REMARK 500 1 DA B 26 0.05 SIDE_CHAIN REMARK 500 1 DT B 27 0.07 SIDE_CHAIN REMARK 500 2 DC A 5 0.06 SIDE_CHAIN REMARK 500 2 DG B 19 0.09 SIDE_CHAIN REMARK 500 2 DT B 27 0.08 SIDE_CHAIN REMARK 500 3 DT A 9 0.06 SIDE_CHAIN REMARK 500 3 DG B 19 0.09 SIDE_CHAIN REMARK 500 3 DG B 25 0.08 SIDE_CHAIN REMARK 500 3 DT B 27 0.07 SIDE_CHAIN REMARK 500 4 DC B 18 0.07 SIDE_CHAIN REMARK 500 4 DG B 19 0.09 SIDE_CHAIN REMARK 500 4 DT B 27 0.08 SIDE_CHAIN REMARK 500 5 DG A 17 0.05 SIDE_CHAIN REMARK 500 5 DG B 19 0.09 SIDE_CHAIN REMARK 500 5 DT B 27 0.08 SIDE_CHAIN REMARK 500 6 DC A 5 0.06 SIDE_CHAIN REMARK 500 6 DG B 19 0.10 SIDE_CHAIN REMARK 500 6 DT B 27 0.07 SIDE_CHAIN REMARK 500 7 DC A 5 0.07 SIDE_CHAIN REMARK 500 7 DG B 19 0.08 SIDE_CHAIN REMARK 500 7 DT B 27 0.06 SIDE_CHAIN REMARK 500 8 DC A 5 0.06 SIDE_CHAIN REMARK 500 8 DC B 18 0.07 SIDE_CHAIN REMARK 500 8 DG B 19 0.07 SIDE_CHAIN REMARK 500 8 DT B 27 0.07 SIDE_CHAIN REMARK 500 9 DG A 17 0.05 SIDE_CHAIN REMARK 500 9 DG B 19 0.09 SIDE_CHAIN REMARK 500 9 DG B 25 0.07 SIDE_CHAIN REMARK 500 9 DT B 27 0.07 SIDE_CHAIN REMARK 500 10 DT A 4 0.08 SIDE_CHAIN REMARK 500 10 DC A 5 0.06 SIDE_CHAIN REMARK 500 10 DG B 19 0.09 SIDE_CHAIN REMARK 500 10 DG B 25 0.06 SIDE_CHAIN REMARK 500 10 DT B 27 0.07 SIDE_CHAIN REMARK 500 11 DA A 3 0.05 SIDE_CHAIN REMARK 500 11 DT A 4 0.07 SIDE_CHAIN REMARK 500 11 DC A 13 0.07 SIDE_CHAIN REMARK 500 11 DG B 19 0.09 SIDE_CHAIN REMARK 500 11 DC B 24 0.07 SIDE_CHAIN REMARK 500 11 DG B 25 0.08 SIDE_CHAIN REMARK 500 11 DT B 27 0.08 SIDE_CHAIN REMARK 500 12 DG A 17 0.07 SIDE_CHAIN REMARK 500 12 DG B 19 0.10 SIDE_CHAIN REMARK 500 12 DT B 27 0.07 SIDE_CHAIN REMARK 500 13 DC A 5 0.06 SIDE_CHAIN REMARK 500 13 DG B 19 0.10 SIDE_CHAIN REMARK 500 13 DT B 27 0.08 SIDE_CHAIN REMARK 500 14 DT A 9 0.06 SIDE_CHAIN REMARK 500 14 DG B 25 0.07 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 0.07 SIDE_CHAIN REMARK 500 15 DG B 19 0.10 SIDE_CHAIN REMARK 500 15 DT B 27 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QSK RELATED DB: PDB REMARK 900 1QSK CONTAINS A SIMILAR PENTANUCLEOTIDE DNA BULGE WITH REMARK 900 AAAAA IN THE BULGE LOOP. REMARK 900 RELATED ID: 1JRW RELATED DB: PDB REMARK 900 1JRW IS THE SOLUTION STRUCTURE OF DAATAA DNA BULGE REMARK 900 (MINIMIZED AVERAGE STRUCTURE) REMARK 900 RELATED ID: 1JS5 RELATED DB: PDB REMARK 900 1JS5 IS THE SOLUTION STRUCTURE OF DAAUAA DNA BULGE REMARK 900 (MINIMIZED AVERAGE STRUCTURE) REMARK 900 RELATED ID: 1JS7 RELATED DB: PDB REMARK 900 1JS7 IS THE SOLUTION STRUCTURE OF DAAUAA DNA BULGE REMARK 900 (ENSEMBLE) DBREF 1JRV A 1 17 PDB 1JRV 1JRV 1 17 DBREF 1JRV B 18 29 PDB 1JRV 1JRV 18 29 SEQRES 1 A 17 DG DC DA DT DC DG DA DA DT 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 220 0 0 0 0 0 0 6 0 0 0 3 END