HEADER DNA 28-AUG-02 1MK6 TITLE SOLUTION STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY- TITLE 2 AFLATOXIN B1 ADDUCT MISPAIRED WITH DEOXYADENOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*AP*GP*AP*TP*AP*GP*AP*TP*GP*T)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES 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 AFLATOXIN B1- GUANINE ADDUCT OPPOSITE AN ADENINE, MIMICKING GA KEYWDS 2 TRANSITION, DNA EXPDTA SOLUTION NMR AUTHOR I.GIRI,D.S.JOHNSTON,M.P.STONE REVDAT 3 30-JAN-19 1MK6 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQRES HET HETNAM FORMUL REVDAT 3 3 1 LINK ATOM REVDAT 2 24-FEB-09 1MK6 1 VERSN REVDAT 1 16-OCT-02 1MK6 0 JRNL AUTH I.GIRI,D.S.JOHNSTON,M.P.STONE JRNL TITL MISPAIRING OF THE JRNL TITL 2 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT WITH JRNL TITL 3 DEOXYADENOSINE RESULTS IN EXTRUSION OF THE MISMATCHED DA JRNL TITL 4 TOWARD THE MAJOR GROOVE JRNL REF BIOCHEMISTRY V. 41 5462 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 11969407 JRNL DOI 10.1021/BI012116T REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 97, 2000, X-PLOR 3.1 REMARK 3 AUTHORS : ACCELYRIS, INC., SAN DIEGO, CA (FELIX), REMARK 3 A.T.BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THERE WERE 329 EXPERIMENTAL DISTANCE REMARK 3 RESTRAINTS DERIVED FROM NONEXCHANGEABLE 1H NOES BY MARDIGRAS. REMARK 3 THESE CONSISTED OF 181 INTRANUCLEOTIDE RESTRAINTS, 110 REMARK 3 INTERNUCLEOTIDE RESTRAINTS, AND 38 ADDUCT-DNA RESTRAINTS REMARK 4 REMARK 4 1MK6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016974. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 273 REMARK 210 PH : 7.4; 7.4 REMARK 210 IONIC STRENGTH : 0.5 ML OF 0.01 M SODIUM REMARK 210 PHOSPHATE CONTAINING 0.1 M NACL REMARK 210 AND 0.05 MM NA2EDTA AT PD 7.4. REMARK 210 THE SAMPLE WAS DISSOLVED IN REMARK 210 99.96% D2O; FOR OBSERVATION OF REMARK 210 EXCHANGEABLE PROTONS, THE SAMPLE REMARK 210 WAS DISSOLVED IN 9:1 H2O:D2O, REMARK 210 BUFFER, CONTAINING 0.01 M SODIUM REMARK 210 PHOSPHATE CONTAINING 0.1 M NACL REMARK 210 AND 0.05 MM NA2EDTA AT PH 7.4 REMARK 210 PRESSURE : ATM; ATM REMARK 210 SAMPLE CONTENTS : 80 OD OF REMARK 210 D(ACATCAFBGATCT)D(AGATAGATGT) REMARK 210 SOLUTION IN NMR BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; P REMARK 210 -COSY; T1 REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 4.0, MARDIGRAS 3.2, REMARK 210 AMBER 6.0, CORMA 4.0, INSIGHTII REMARK 210 2000, GAUSSIAN 98 1998 REMARK 210 METHOD USED : DISTANCE GEOMETRY : MARDIGRAS; REMARK 210 SIMULATED ANNEALING MOLECULAR REMARK 210 DYNAMICS : XPLOR; AVERAGE REMARK 210 STRUCTURE CALCULATION ADDITION REMARK 210 OF SOLVENT, AND COUNTERIONS : REMARK 210 AMBER; SIMULATED ANNEALING AND REMARK 210 MOLECULAR DYNAMICS MATRIX REMARK 210 RELAXATION : CORMA; REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : FINAL CALCULATED STRUCTURE IS REMARK 210 BEING SUBMITTED. BACK CALCULATED REMARK 210 STRUCTURE IS IN AGREEMENT WITH REMARK 210 NOESY DATA. THE CALCULATION WAS REMARK 210 PERFORMED IN PRESENCE OF SOLVENT REMARK 210 AND COUNTERIONS. SOLVENT, AND REMARK 210 COUNTERION CO-ORDINATES ARE NOT REMARK 210 BEING REPORTED, ONLY THE DUPLEX REMARK 210 DNA. BEFORE SOLVATING AND REMARK 210 ADDITION OF COUNTER IONS, 20 REMARK 210 FINAL STRUCTURES WERE CALCULATED REMARK 210 USING XPLOR. THE FINAL AVERAGED REMARK 210 ENERGY MINIMIZED STRUCTURE WAS REMARK 210 SOLVATED, AND THE COUNTER IONS REMARK 210 WERE ADDED TO IT. THEN MD WAS REMARK 210 RAN FOR 1.4 NS TIME SCALE TO REMARK 210 OBTAIN FINAL STRUCTURE. REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: 40 STRUCTURES WERE CALCULATED STARTING FROM B AND A FORM REMARK 210 DNA. 20 CLOSELY CONVERGENT FROM BOTH WAS AVERAGED, AND RMSD REMARK 210 VALUE WAS CHECKED. THE FINAL AVERAGED STRUCTURE WAS CALCULATED REMARK 210 BY AVERAGING FINAL A AND FINAL B, AND AFTER ENERGY MINIMIZATION. REMARK 210 THIS ENERGY MINIMIZED STRUCTURE WAS SOLVATED, AND EXPLICIT REMARK 210 COUNTERIONS WERE ADDED. IN ALL, 17 NA+ IONS WERE ADDED TO REMARK 210 NEUTRALIZE THE SYSTEM USING THE LEAP MODULE IN AMBER 6.0. THE REMARK 210 SHAKE ALGORITHM CONSTRAINED BONDS INVOLVING PROTONS TO A REMARK 210 TOLERANCE OF 0.0005 . A 1 FS TIME STEP WAS USED. THE RMD REMARK 210 CALCULATIONS WERE RUN FOR 1.4 NS, AND COORDINATES WERE CAPTURED REMARK 210 EVERY 200 PS. THE EMERGENT STRUCTURE FROM AMBER IS BEING REPORTED 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 DA A 1 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA A 3 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA A 7 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC A 9 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC A 9 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT A 10 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT A 10 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 DA B 11 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT B 14 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 DA B 15 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA B 15 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT B 20 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT B 20 C6 - C5 - C7 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 DA B 15 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MKL RELATED DB: PDB REMARK 900 NMR REFINED STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY- REMARK 900 AFLATOXIN B1 ADDUCT IN A 5'-CPAFBG-3' SEQUENCE DBREF 1MK6 A 1 10 PDB 1MK6 1MK6 1 10 DBREF 1MK6 B 11 20 PDB 1MK6 1MK6 11 20 SEQRES 1 A 10 DA DC DA DT DC DG DA DT DC DT SEQRES 1 B 10 DA DG DA DT DA DG DA DT DG DT HET AFN A 11 37 HETNAM AFN 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1 FORMUL 3 AFN C17 H14 O7 LINK N7 DG A 6 C8A AFN A 11 1555 1555 1.51 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