HEADER DNA 20-APR-01 1II1 TITLE STRUCTURAL BASIS FOR POOR URACIL EXCISION FROM HAIRPIN DNA: TITLE 2 NMR STUDY COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 D(*AP*GP*GP*AP*TP*CP*CP*UP*TP*TP*TP*GP*GP*AP*TP*CP*CP*T)- COMPND 4 3'; COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: URACIL CONTAINING HAIRPIN DNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CUSTOM MADE RANSOM HILL BIOSCIENCES, INC., SOURCE 4 RAMONA CA (USA) KEYWDS URACIL, HAIRPIN DNA, HAIRPIN LOOP, DOUBLE HELIX, UDG-URACIL KEYWDS 2 INTERACTION EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.GHOSH,N.RUMPAL,U.VARSHNEY,K.V.CHARY REVDAT 3 24-FEB-09 1II1 1 VERSN REVDAT 2 01-APR-03 1II1 1 JRNL REVDAT 1 08-MAY-02 1II1 0 JRNL AUTH M.GHOSH,N.RUMPAL,U.VARSHNEY,K.V.CHARY JRNL TITL STRUCTURAL BASIS FOR POOR URACIL EXCISION FROM JRNL TITL 2 HAIRPIN DNA. AN NMR STUDY. JRNL REF EUR.J.BIOCHEM. V. 269 1886 2002 JRNL REFN ISSN 0014-2956 JRNL PMID 11952790 JRNL DOI 10.1046/J.1432-1033.2002.02837.X REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 97 REMARK 3 AUTHORS : MSI REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON TOTAL OF REMARK 3 227 RESTRAINTS, 143 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 64 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 10 DISTANCE RESTRAINTS FROM REMARK 3 HYDROGEN BONDS. REMARK 4 REMARK 4 1II1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-01. REMARK 100 THE RCSB ID CODE IS RCSB013285. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 305; 295 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 2 MM OLIGO; NO BUFFER; PH = REMARK 210 7.0; 305K; 99% D2O; 2 MM REMARK 210 OLIGO; NO BUFFER; PH = 7.0; REMARK 210 305K; 90% H2O + 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, E-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS, AMX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN, BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1, DISCOVER 97, UXNMR REMARK 210 3.0, FELIX 97 REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 AND ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND REMARK 210 ENERGY,STRUCTURES WITH THE REMARK 210 LEAST RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR REMARK 210 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 2 DT A 9 C5 DT A 9 C7 0.036 REMARK 500 REMARK 500 REMARK: NULL 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 DA A 1 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 1 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 1 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DG A 2 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 3 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 5 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 13.0 DEGREES REMARK 500 1 DC A 6 C6 - N1 - C2 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DU A 8 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DU A 8 C5 - C6 - N1 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT A 9 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DT A 1B C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT A 2B O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 2B C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG A 3B O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DG A 4B O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 4B C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA A 5B C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 5B C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 5B N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DT A 6B O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DT A 6B C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC A 7B O4' - C1' - N1 ANGL. DEV. = 10.4 DEGREES REMARK 500 1 DC A 8B O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 9B N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 9B C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DA A 1 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 2 DA A 1 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DA A 1 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DA A 1 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 DG A 2 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT A 5 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 12.9 DEGREES REMARK 500 2 DC A 6 C6 - N1 - C2 ANGL. DEV. = -2.4 DEGREES REMARK 500 2 DC A 7 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 312 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 DG A 2 0.08 SIDE_CHAIN REMARK 500 1 DC A 6 0.19 SIDE_CHAIN REMARK 500 1 DC A 7 0.31 SIDE_CHAIN REMARK 500 1 DT A 9 0.15 SIDE_CHAIN REMARK 500 1 DG A 3B 0.07 SIDE_CHAIN REMARK 500 2 DG A 2 0.07 SIDE_CHAIN REMARK 500 2 DG A 3 0.07 SIDE_CHAIN REMARK 500 2 DC A 6 0.19 SIDE_CHAIN REMARK 500 2 DC A 7 0.30 SIDE_CHAIN REMARK 500 2 DT A 9 0.14 SIDE_CHAIN REMARK 500 2 DG A 3B 0.08 SIDE_CHAIN REMARK 500 3 DC A 6 0.20 SIDE_CHAIN REMARK 500 3 DC A 7 0.31 SIDE_CHAIN REMARK 500 3 DT A 9 0.15 SIDE_CHAIN REMARK 500 3 DG A 3B 0.08 SIDE_CHAIN REMARK 500 3 DT A 9B 0.09 SIDE_CHAIN REMARK 500 4 DC A 6 0.20 SIDE_CHAIN REMARK 500 4 DC A 7 0.31 SIDE_CHAIN REMARK 500 4 DT A 9 0.13 SIDE_CHAIN REMARK 500 4 DG A 3B 0.08 SIDE_CHAIN REMARK 500 4 DT A 9B 0.09 SIDE_CHAIN REMARK 500 5 DC A 6 0.19 SIDE_CHAIN REMARK 500 5 DC A 7 0.30 SIDE_CHAIN REMARK 500 5 DT A 9 0.14 SIDE_CHAIN REMARK 500 5 DG A 3B 0.08 SIDE_CHAIN REMARK 500 5 DC A 8B 0.08 SIDE_CHAIN REMARK 500 5 DT A 9B 0.08 SIDE_CHAIN REMARK 500 6 DA A 1 0.05 SIDE_CHAIN REMARK 500 6 DC A 6 0.19 SIDE_CHAIN REMARK 500 6 DC A 7 0.31 SIDE_CHAIN REMARK 500 6 DT A 9 0.13 SIDE_CHAIN REMARK 500 6 DG A 3B 0.08 SIDE_CHAIN REMARK 500 6 DT A 9B 0.08 SIDE_CHAIN REMARK 500 7 DG A 2 0.07 SIDE_CHAIN REMARK 500 7 DG A 3 0.06 SIDE_CHAIN REMARK 500 7 DC A 6 0.18 SIDE_CHAIN REMARK 500 7 DC A 7 0.31 SIDE_CHAIN REMARK 500 7 DT A 9 0.11 SIDE_CHAIN REMARK 500 7 DG A 3B 0.08 SIDE_CHAIN REMARK 500 7 DC A 7B 0.09 SIDE_CHAIN REMARK 500 8 DC A 6 0.19 SIDE_CHAIN REMARK 500 8 DC A 7 0.31 SIDE_CHAIN REMARK 500 8 DT A 9 0.12 SIDE_CHAIN REMARK 500 8 DG A 3B 0.07 SIDE_CHAIN REMARK 500 8 DC A 7B 0.08 SIDE_CHAIN REMARK 500 8 DT A 9B 0.09 SIDE_CHAIN REMARK 500 9 DC A 6 0.18 SIDE_CHAIN REMARK 500 9 DC A 7 0.31 SIDE_CHAIN REMARK 500 9 DT A 9 0.14 SIDE_CHAIN REMARK 500 9 DG A 3B 0.07 SIDE_CHAIN REMARK 500 9 DC A 7B 0.09 SIDE_CHAIN REMARK 500 9 DT A 9B 0.09 SIDE_CHAIN REMARK 500 10 DC A 6 0.20 SIDE_CHAIN REMARK 500 10 DC A 7 0.31 SIDE_CHAIN REMARK 500 10 DT A 9 0.13 SIDE_CHAIN REMARK 500 10 DG A 3B 0.08 SIDE_CHAIN REMARK 500 10 DT A 9B 0.09 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QE7 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A URACIL CONTAINING HAIRPIN DNA REMARK 900 RELATED ID: 1DGO RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR URACIL DNA GLYCOSYLASE INTERACTION REMARK 900 WITH URACIL: NMR STUDY REMARK 900 RELATED ID: 1IDX RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR POOR URACIL EXCISION FROM HAIRPIN DNA: REMARK 900 NMR STUDY REMARK 900 RELATED ID: 4536 RELATED DB: BMRB REMARK 900 STRUCTURAL BASIS FOR URACIL DNA GLYCOSYLASE INTERACTION REMARK 900 WITH URACIL: NMR STUDY DBREF 1II1 A 1 9B PDB 1II1 1II1 1 9 SEQRES 1 A 18 DA DG DG DA DT DC DC DU DT DT DT DG DG SEQRES 2 A 18 DA DT DC DC DT 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 MASTER 234 0 0 0 0 0 0 6 0 0 0 2 END