HEADER DNA 17-JUL-06 2HPX TITLE 13MER DUPLEX DNA CONTAINING A 4'-OXIDIZED ABASIC SITE, AVERAGED TITLE 2 STRUCTURE CAVEAT 2HPX CHIRALITY ERROR AT C1' OF X4A COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*AP*AP*GP*(X4A)P*AP*CP*CP*GP*GP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: STRAND CONTAINING 4'-OXIDIZED ABASIC SITE; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: TEMPLATE STRAND SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS ABASIC SITE, DNA DAMAGE, BLEOMYCIN, MOLECULAR DYNAMICS, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR J.CHEN,F.Y.DUPRADEAU,D.A.CASE,C.J.TURNER,J.STUBBE REVDAT 3 08-AUG-18 2HPX 1 SOURCE REMARK REVDAT 2 24-FEB-09 2HPX 1 VERSN REVDAT 1 29-MAY-07 2HPX 0 JRNL AUTH J.CHEN,F.Y.DUPRADEAU,D.A.CASE,C.J.TURNER,J.STUBBE JRNL TITL NUCLEAR MAGNETIC RESONANCE STRUCTURAL STUDIES AND MOLECULAR JRNL TITL 2 MODELING OF DUPLEX DNA CONTAINING NORMAL AND 4'-OXIDIZED JRNL TITL 3 ABASIC SITES. JRNL REF BIOCHEMISTRY V. 46 3096 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17323932 JRNL DOI 10.1021/BI6024269 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 8.0 REMARK 3 AUTHORS : CASE, D.A. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON 410 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 43 DIHEDRAL ANGLE RESTRAINTS,8 DISTANCE REMARK 3 RESTRAINTS REMARK 3 FROM HYDROGEN BONDS. REMARK 4 REMARK 4 2HPX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1000038621. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 277 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 10 MM SODIUM PHOSPHATE; 10 MM REMARK 210 SODIUM PHOSPHATE REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 2.0 MM DUPLEX DNA CONTAINING A REMARK 210 4'-OXIDIZED ABASIC SITE, 10 MM REMARK 210 SODIUM PHOSPHATE, 0.2 MM EDTA, REMARK 210 100% D2O; 2.0 MM DUPLEX DNA REMARK 210 CONTAINING A 4'-OXIDIZED ABASIC REMARK 210 SITE, 0.2 MM EDTA, 90%D2O/10% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; E-COSY; PH REMARK 210 -COSY; HP-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 591 MHZ REMARK 210 SPECTROMETER MODEL : CUSTOM-BUILT REMARK 210 SPECTROMETER MANUFACTURER : HOME-BUILT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000, MARDIGRAS REMARK 210 METHOD USED : SIMULATED ANNEALING MATRIX REMARK 210 RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE MODEL 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 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 3 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA A 8 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 DA A 8 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC A 9 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DC A 10 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 14 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC B 15 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 DC B 16 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT B 19 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 DA B 20 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA B 20 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA B 20 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA B 20 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 DC B 21 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT B 22 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT B 22 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT B 23 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT B 24 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG B 26 O4' - C1' - N9 ANGL. DEV. = 2.6 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 DG A 6 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HOU RELATED DB: PDB REMARK 900 13MER DUPLEX DNA CONTAINING A 4'-OXIDIZED ABASIC SITE, 10 STRUCTURES DBREF 2HPX A 1 13 PDB 2HPX 2HPX 1 13 DBREF 2HPX B 14 26 PDB 2HPX 2HPX 14 26 SEQRES 1 A 13 DC DC DA DA DA DG X4A DA DC DC DG DG DG SEQRES 1 B 13 DC DC DC DG DG DT DA DC DT DT DT DG DG HET X4A A 7 21 HETNAM X4A [(2R,3S,5S)-2,3,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL HETNAM 2 X4A DIHYDROGEN PHOSPHATE FORMUL 1 X4A C5 H11 O8 P LINK O3' DG A 6 P X4A A 7 1555 1555 1.59 LINK O3' X4A A 7 P DA A 8 1555 1555 1.61 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 MASTER 147 0 1 0 0 0 0 6 0 0 0 2 END