10 20 30 40 50 60 70 80 1JS5 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 16-AUG-01 1JS5
TITLE SOLUTION STRUCTURE OF DAAUAA DNA BULGE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 D(*GP*CP*AP*TP*CP*GP*AP*AP*UP*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
MDLTYP MINIMIZED AVERAGE
AUTHOR F.A.GOLLMICK,M.LORENZ,U.DORNBERGER,J.VON LANGEN,S.DIEKMANN, AUTHOR 2 H.FRITZSCHE
REVDAT 2 24-FEB-09 1JS5 1 VERSN REVDAT 1 28-AUG-02 1JS5 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 932 RESTRAINTS, 671 ARE NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 235 DIHEDRAL ANGLE RESTRAINTS,26 DISTANCE RESTRAINTS FROM REMARK 3 HYDROGEN BONDS.
REMARK 4 REMARK 4 1JS5 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 RCSB ID CODE IS RCSB014125.
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 REMARK 210 PHOSPHATE BUFFER; 100 MM NACL; REMARK 210 0.05MM EDTA, 100% D2O; 3.8MM REMARK 210 IN DUPLEX; 100 MM NACL; 0.05MM REMARK 210 EDTA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL 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 : NMRPIPE 3, MARDIGRAS 3.2, REMARK 210 DYANA 1.5, AMBER 5.0 REMARK 210 METHOD USED : MATRIX RELAXATION, TORSION REMARK 210 ANGLE DYNAMICS, ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE FINAL AVERAGE STRUCTURE WAS OBTAINED BY COORDINATE REMARK 210 AVERAGING OF THE FINAL ENSEMBLE OF STRUCTURES, FOLLOWED BY REMARK 210 RESTRAINED ENERGY MINIMIZATION. THIS STRUCTURE WAS DETERMINED REMARK 210 USING STANDARD 2D 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 DT A 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 7 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DU A 9 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA A 10 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 DA A 11 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC A 16 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 DA B 21 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC B 23 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG B 25 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT B 27 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG B 28 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES 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 DC A 2 0.06 SIDE_CHAIN REMARK 500 DA A 3 0.05 SIDE_CHAIN REMARK 500 DC A 13 0.06 SIDE_CHAIN REMARK 500 DT A 14 0.07 SIDE_CHAIN REMARK 500 DG B 19 0.12 SIDE_CHAIN REMARK 500 DT B 20 0.07 SIDE_CHAIN REMARK 500 DC B 24 0.06 SIDE_CHAIN REMARK 500 DG B 25 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 PENTANUCLEOTIDEDNA BULGE WITH AAAAA REMARK 900 IN THE BULGE LOOP REMARK 900 RELATED ID: 1JRV RELATED DB: PDB REMARK 900 1JRV CONTAINS A SIMILAR PENTANUCLEOTIDEDNA BULGE WITH AATAA REMARK 900 IN THE 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: 1JS7 RELATED DB: PDB REMARK 900 1JS7 IS THE SOLUTION STRUCTURE (ENSEMBLE) OF DAAUAA DNA REMARK 900 BULGE
DBREF 1JS5 A 1 17 PDB 1JS5 1JS5 1 17 DBREF 1JS5 B 18 29 PDB 1JS5 1JS5 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 1.000 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