PDB Short entry for 1AG5 HEADER DNA 01-APR-97 1AG5 TITLE THE SOLUTION STRUCTURE OF AN AFLATOXIN B1 EPOXIDE ADDUCT AT THE N7 TITLE 2 POSITION OF GUANINE OPPOSITE AN ADENINE IN THE COMPLEMENTARY STRAND TITLE 3 OF AN OLIGODEOXYNUCLEOTIDE DUPLEX, NMR, MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*AP*TP*CP*GP*AP*TP*CP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXYAFLATOXIN B1 COMPND 6 OPPOSITE CPA IN THE COMPLEMENTARY STRAND; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*GP*AP*TP*CP*AP*GP*AP*TP*GP*G)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXYAFLATOXIN B1 COMPND 12 OPPOSITE CPA IN THE COMPLEMENTARY 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 AFLATOXIN B1, N7-GUANINE ADDUCT, INTERCALATION, DNA DUPLEX, KEYWDS 2 DEOXYRIBONUCLEIC ACID, DNA EXPDTA SOLUTION NMR AUTHOR D.S.JOHNSON,M.P.STONE REVDAT 4 10-APR-24 1AG5 1 REMARK LINK REVDAT 3 30-JAN-19 1AG5 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQRES HET HETNAM FORMUL REVDAT 3 3 1 LINK ATOM REVDAT 2 24-FEB-09 1AG5 1 VERSN REVDAT 1 17-SEP-97 1AG5 0 JRNL AUTH D.S.JOHNSTON,M.P.STONE JRNL TITL REFINED SOLUTION STRUCTURE OF JRNL TITL 2 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXYAFLATOXIN B1 OPPOSITE CPA JRNL TITL 3 IN THE COMPLEMENTARY STRAND OF AN OLIGODEOXYNUCLEOTIDE JRNL TITL 4 DUPLEX AS DETERMINED BY 1H NMR. JRNL REF BIOCHEMISTRY V. 34 14037 1995 JRNL REFN ISSN 0006-2960 JRNL PMID 7578001 JRNL DOI 10.1021/BI00043A009 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 1AG5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170774. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; 2QF-COSY; AND TOCSY; : REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX, X-PLOR, MARDIGRAS, CORMA REMARK 210 METHOD USED : NOE-RESTRAINED MOLECULAR REMARK 210 DYNAMICS/SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : THIS STRUCTURE PROVIDED THE BEST REMARK 210 -FIT FOR THE NOE DATA BASED ON REMARK 210 THE RELAXATION MATRIX ANALYSIS REMARK 210 USING CORMA REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL 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 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG A 6 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG A 6 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA A 7 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B 11 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG B 11 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG B 11 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 12 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG B 12 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DA B 13 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA B 13 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA B 16 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA B 16 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG B 17 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 17 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG B 17 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DA B 18 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA B 18 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 20 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 20 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG B 20 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 DG B 21 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B 21 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG B 21 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 1AG5 A 1 10 PDB 1AG5 1AG5 1 10 DBREF 1AG5 B 11 21 PDB 1AG5 1AG5 11 21 SEQRES 1 A 10 DC DC DA DT DC DG DA DT DC DC SEQRES 1 B 11 DG DG DA DT DC DA DG DA DT DG DG 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 1.49 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