HEADER DNA 05-APR-01 1IDX TITLE STRUCTURAL BASIS FOR POOR EXCISION FROM HAIRPIN DNA: NMR STUDY COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*TP*UP*TP*GP*GP*AP*TP*CP*CP*T) COMPND 3 -3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: URACIL CONTAINING HAIRPIN DNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CUSTOM MADE BY RANSOM HILL BIOSCIENCES, INC., RAMONA SOURCE 4 CA (USA) KEYWDS URACIL, HAIRPIN DNA, HAIRPIN LOOP, DOUBLE HELIX, UDG-URACIL KEYWDS 2 INTERACTION, DNA EXPDTA SOLUTION NMR NUMMDL 6 AUTHOR M.GHOSH,N.RUMPAL,U.VARSHNEY,K.V.CHARY REVDAT 4 23-FEB-22 1IDX 1 REMARK REVDAT 3 24-FEB-09 1IDX 1 VERSN REVDAT 2 01-APR-03 1IDX 1 JRNL REVDAT 1 08-MAY-02 1IDX 0 JRNL AUTH M.GHOSH,N.RUMPAL,U.VARSHNEY,K.V.CHARY JRNL TITL STRUCTURAL BASIS FOR POOR URACIL EXCISION FROM HAIRPIN DNA. JRNL TITL 2 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, DISCOVER 97 REMARK 3 AUTHORS : VARIAN (VNMR), MSI (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 196 RESTRAINTS, 122 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 64 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 10 DISTANCE RESTRAINTS FROM HYDROGEN REMARK 3 BONDS. REMARK 4 REMARK 4 1IDX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013191. 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 = 7.0; REMARK 210 305K; 99% D2O; 2 MM OLIGO; NO REMARK 210 BUFFER; PH = 7.0; 305K; 90% H2O + REMARK 210 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 : DISCOVER 97, VNMR 6.1, 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 : 6 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND ENERGY, REMARK 210 STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST 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 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 1 DU A 1B N1 DU A 1B C6 0.102 REMARK 500 2 DU A 1B N1 DU A 1B C6 0.103 REMARK 500 3 DU A 1B N1 DU A 1B C6 0.103 REMARK 500 4 DU A 1B N1 DU A 1B C6 0.101 REMARK 500 5 DU A 1B N1 DU A 1B C6 0.102 REMARK 500 6 DU A 1B N1 DU A 1B C6 0.103 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' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA A 1 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 1 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 8 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT A 8 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DT A 9 C6 - N1 - C2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DT A 9 C2 - N3 - C4 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 9 C5 - C6 - N1 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT A 9 C6 - N1 - C1' ANGL. DEV. = 10.6 DEGREES REMARK 500 1 DU A 1B O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DU A 1B N1 - C2 - N3 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DU A 1B N3 - C2 - O2 ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DT A 2B O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 2B N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DT A 2B C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 3B O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG A 3B O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DG A 4B O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA A 5B O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DA A 5B C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 6B O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 6B N3 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT A 6B C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DC A 7B O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC A 8B O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DT A 9B N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 9B C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DA A 1 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA A 1 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA A 1 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DG A 2 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DG A 2 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA A 4 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 223 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 DT A 8 0.09 SIDE CHAIN REMARK 500 1 DT A 9 0.42 SIDE CHAIN REMARK 500 1 DT A 2B 0.07 SIDE CHAIN REMARK 500 1 DG A 3B 0.06 SIDE CHAIN REMARK 500 2 DG A 2 0.07 SIDE CHAIN REMARK 500 2 DT A 8 0.09 SIDE CHAIN REMARK 500 2 DT A 9 0.40 SIDE CHAIN REMARK 500 2 DT A 2B 0.15 SIDE CHAIN REMARK 500 2 DG A 3B 0.06 SIDE CHAIN REMARK 500 3 DA A 1 0.06 SIDE CHAIN REMARK 500 3 DG A 2 0.06 SIDE CHAIN REMARK 500 3 DT A 8 0.08 SIDE CHAIN REMARK 500 3 DT A 9 0.43 SIDE CHAIN REMARK 500 3 DT A 2B 0.07 SIDE CHAIN REMARK 500 4 DG A 2 0.08 SIDE CHAIN REMARK 500 4 DT A 8 0.09 SIDE CHAIN REMARK 500 4 DT A 9 0.41 SIDE CHAIN REMARK 500 4 DT A 2B 0.08 SIDE CHAIN REMARK 500 4 DG A 3B 0.07 SIDE CHAIN REMARK 500 4 DT A 6B 0.08 SIDE CHAIN REMARK 500 5 DG A 2 0.08 SIDE CHAIN REMARK 500 5 DT A 8 0.09 SIDE CHAIN REMARK 500 5 DT A 9 0.42 SIDE CHAIN REMARK 500 5 DT A 2B 0.07 SIDE CHAIN REMARK 500 5 DG A 3B 0.06 SIDE CHAIN REMARK 500 6 DG A 2 0.07 SIDE CHAIN REMARK 500 6 DT A 8 0.09 SIDE CHAIN REMARK 500 6 DT A 9 0.40 SIDE CHAIN REMARK 500 6 DT A 2B 0.15 SIDE CHAIN REMARK 500 6 DG A 3B 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1II1 RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR POOR URACIL EXCISION FROM HAIRPIN DNA: NMR REMARK 900 STUDY 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 WITH URACIL: REMARK 900 NMR STUDY REMARK 900 RELATED ID: 4536 RELATED DB: BMRB REMARK 900 STRUCTURAL BASIS FOR URACIL DNA GLYCOSYLASE INTERACTION WITH URACIL: REMARK 900 NMR STUDY DBREF 1IDX A 1 9B PDB 1IDX 1IDX 1 9 SEQRES 1 A 18 DA DG DG DA DT DC DC DT DT DU 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 MODEL 1