PDB Short entry for 1JS7 HEADER DNA 16-AUG-01 1JS7 TITLE SOLUTION STRUCTURE OF DAAUAA DNA BULGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*AP*TP*CP*GP*AP*AP*UP*AP*AP*GP*CP*TP*AP*CP*G)- COMPND 3 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, DNA EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR F.A.GOLLMICK,M.LORENZ,U.DORNBERGER,J.VON LANGEN,S.DIEKMANN, AUTHOR 2 H.FRITZSCHE REVDAT 4 23-FEB-22 1JS7 1 REMARK REVDAT 3 24-FEB-09 1JS7 1 VERSN REVDAT 2 01-APR-03 1JS7 1 JRNL REVDAT 1 19-JUN-02 1JS7 0 JRNL AUTH F.A.GOLLMICK,M.LORENZ,U.DORNBERGER,J.VON LANGEN,S.DIEKMANN, JRNL AUTH 2 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 3, AMBER 5.0 REMARK 3 AUTHORS : DELAGLIO ET AL. (NMRPIPE), WEINER, S.J., KOLLMAN, REMARK 3 P.A., NGUYEN, D.T., CASE, D.A. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 932 RESTRAINTS, 671 ARE NOE- REMARK 3 DERIVED REMARK 3 DISTANCE CONSTRAINTS, 235 DIHEDRAL ANGLE RESTRAINTS, 26 DISTANCE REMARK 3 RESTRAINTS REMARK 3 FROM HYDROGEN BONDS. REMARK 4 REMARK 4 1JS7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-AUG-01. REMARK 100 THE DEPOSITION ID IS D_1000014127. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300; 300 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : 100MM NA+; 100MM NA+ REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 3.8MM IN DUPLEX; 10MM PHOSPHATE REMARK 210 BUFFER; 100 MM NACL; 0.05MM EDTA, REMARK 210 100% D2O; 3.8MM IN DUPLEX; 100 REMARK 210 MM NACL; 0.05MM EDTA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D_NOESY; E-COSY; 31P REMARK 210 -1H_HETERONUCLEAR_CORRELATED REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MARDIGRAS 3.2, DYANA 1.5, AMBER REMARK 210 5.0 REMARK 210 METHOD USED : MATRIX RELAXATION, TORSION ANGLE REMARK 210 DYNAMICS, ENERGY MINIMIZATION 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 : NULL 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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 7 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DA A 8 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DU A 9 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 10 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DA A 11 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC A 16 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DA B 21 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DC B 23 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DG B 25 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT B 27 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG B 28 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DA A 7 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DA A 8 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DU A 9 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DA A 10 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 2 DA A 10 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 DA A 11 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DC A 16 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC B 18 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 DA B 21 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG B 22 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DC B 23 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DG B 25 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT B 27 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG B 28 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 DA A 7 C1' - O4' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 3 DA A 7 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DU A 9 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DA A 10 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 298 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 DC A 2 0.06 SIDE CHAIN REMARK 500 1 DT A 4 0.07 SIDE CHAIN REMARK 500 1 DT A 14 0.08 SIDE CHAIN REMARK 500 1 DA A 15 0.06 SIDE CHAIN REMARK 500 1 DG B 19 0.10 SIDE CHAIN REMARK 500 1 DT B 20 0.06 SIDE CHAIN REMARK 500 1 DG B 25 0.07 SIDE CHAIN REMARK 500 2 DC A 13 0.06 SIDE CHAIN REMARK 500 2 DT A 14 0.07 SIDE CHAIN REMARK 500 2 DG B 19 0.10 SIDE CHAIN REMARK 500 2 DT B 20 0.07 SIDE CHAIN REMARK 500 2 DC B 24 0.06 SIDE CHAIN REMARK 500 2 DG B 25 0.08 SIDE CHAIN REMARK 500 3 DT A 4 0.06 SIDE CHAIN REMARK 500 3 DT A 14 0.08 SIDE CHAIN REMARK 500 3 DA A 15 0.06 SIDE CHAIN REMARK 500 3 DG B 19 0.10 SIDE CHAIN REMARK 500 3 DT B 20 0.06 SIDE CHAIN REMARK 500 3 DG B 25 0.07 SIDE CHAIN REMARK 500 4 DC A 2 0.06 SIDE CHAIN REMARK 500 4 DT A 14 0.07 SIDE CHAIN REMARK 500 4 DG B 19 0.11 SIDE CHAIN REMARK 500 4 DT B 20 0.07 SIDE CHAIN REMARK 500 4 DC B 24 0.06 SIDE CHAIN REMARK 500 4 DG B 25 0.07 SIDE CHAIN REMARK 500 5 DT A 14 0.06 SIDE CHAIN REMARK 500 5 DG B 19 0.09 SIDE CHAIN REMARK 500 5 DT B 20 0.07 SIDE CHAIN REMARK 500 5 DG B 25 0.08 SIDE CHAIN REMARK 500 6 DT A 14 0.06 SIDE CHAIN REMARK 500 6 DG B 19 0.08 SIDE CHAIN REMARK 500 6 DT B 20 0.07 SIDE CHAIN REMARK 500 6 DG B 25 0.08 SIDE CHAIN REMARK 500 7 DA A 7 0.06 SIDE CHAIN REMARK 500 7 DG B 19 0.08 SIDE CHAIN REMARK 500 7 DT B 20 0.07 SIDE CHAIN REMARK 500 7 DG B 25 0.08 SIDE CHAIN REMARK 500 8 DT A 4 0.06 SIDE CHAIN REMARK 500 8 DT A 14 0.08 SIDE CHAIN REMARK 500 8 DA A 15 0.06 SIDE CHAIN REMARK 500 8 DG B 19 0.10 SIDE CHAIN REMARK 500 8 DT B 20 0.07 SIDE CHAIN REMARK 500 8 DC B 24 0.06 SIDE CHAIN REMARK 500 8 DG B 25 0.07 SIDE CHAIN REMARK 500 9 DA A 3 0.06 SIDE CHAIN REMARK 500 9 DA A 7 0.05 SIDE CHAIN REMARK 500 9 DC A 13 0.07 SIDE CHAIN REMARK 500 9 DT A 14 0.07 SIDE CHAIN REMARK 500 9 DA A 15 0.05 SIDE CHAIN REMARK 500 9 DG B 19 0.09 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 87 PLANE DEVIATIONS. 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 PENTANUCLEOTIDEDNA BULGE WITH AAAAA IN THE REMARK 900 BULGE LOOP REMARK 900 RELATED ID: 1JRV RELATED DB: PDB REMARK 900 1JRV CONTAINS A SIMILAR PENTANUCLEOTIDEDNA BULGE WITH AATAA IN THE REMARK 900 BULGE LOOP REMARK 900 RELATED ID: 1JRW RELATED DB: PDB REMARK 900 1JRW IS THE AVERAGE SOLUTION STRUCTURE OF DAATAA DNA BULGE REMARK 900 RELATED ID: 1JS5 RELATED DB: PDB REMARK 900 1JS5 IS THE AVERAGE SOLUTION STRUCTURE OF DAAUAA DNA BULGE DBREF 1JS7 A 1 17 PDB 1JS7 1JS7 1 17 DBREF 1JS7 B 18 29 PDB 1JS7 1JS7 18 29 SEQRES 1 A 17 DG DC DA DT DC DG DA DA DU 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 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