10 20 30 40 50 60 70 80 1MKL - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 29-AUG-02 1MKL
TITLE NMR REFINED STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9- TITLE 2 HYDROXY-AFLATOXIN B1 ADDUCT IN A 5'-CPAFBG-3' SEQUENCE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*CP*AP*TP*CP*(X)P*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*CP*GP*AP*TP*GP*T)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES
KEYWDS STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY- KEYWDS 2 AFLATOXIN B1 ADDUCT IN A 5'-CPAFBG-3' SEQUENCE CONTEXT, DNA
EXPDTA SOLUTION NMR
AUTHOR I.GIRI,M.D.JENKINS,N.C.SCHNETZ-BOUTAUD,M.P.STONE
REVDAT 2 24-FEB-09 1MKL 1 VERSN REVDAT 1 16-OCT-02 1MKL 0
JRNL AUTH I.GIRI,M.D.JENKINS,N.C.SCHNETZ-BOUTAUD,M.P.STONE JRNL TITL STRUCTURAL REFINEMENT OF THE JRNL TITL 2 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B(1) JRNL TITL 3 ADDUCT IN A 5'-CP(AFB)G-3' SEQUENCE. JRNL REF CHEM.RES.TOXICOL. V. 15 638 2002 JRNL REFN ISSN 0893-228X JRNL PMID 12018984 JRNL DOI 10.1021/TX010187N
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : A.T.BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 341 REMARK 3 DISTANCE RETRAINTS, 38 EMPIRICAL H-BOND RESTRAINTS, 17 SUGAR REMARK 3 PUCKER RESTRAINTS, AND 89 EMPIRICAL TORSION ANGLE RESTRAINTS
REMARK 4 REMARK 4 1MKL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-02. REMARK 100 THE RCSB ID CODE IS RCSB016986.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 283 REMARK 210 PH : 7.2; 7.2 REMARK 210 IONIC STRENGTH : 0.5 ML OF 0.01 M SODIUM REMARK 210 PHOSPHATE BUFFER CONTAINING REMARK 210 0.1 M NACL AND 0.05 MM NA2EDTA REMARK 210 AT PD 7.2, IN 99.999% D2O; 0.5 REMARK 210 ML OF 0.01 M SODIUM PHOSPHATE REMARK 210 BUFFER CONTAINING 0.1 M NACL REMARK 210 AND 0.05 MM NA2EDTA AT PH 7.2, REMARK 210 IN 9:1 H2O:D2O REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : NULL; NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.0, FELIX 97, REMARK 210 MARDIGRAS 5.2, CORMA 5.2, REMARK 210 AMBER 6.0 REMARK 210 METHOD USED : DATA WAS PROCESSED USING REMARK 210 FELIX 97. THE NOE INTENSITIES REMARK 210 WERE CONVERTED TO DISTANCE REMARK 210 USING RANMARDI MODULE OF REMARK 210 MARDIGRAS. STARTING STRUCTURES REMARK 210 WERE BUILT USING INSIGHTII. REMARK 210 XPLOR WAS USED FOR STRUCTURAL REMARK 210 REFINEMENT. FINAL AVERAGED REMARK 210 STRUCTURE WAS SOLVATED USING REMARK 210 AMBER. AND MD SIMULATED REMARK 210 ANNEALING WAS PERFORMED IN REMARK 210 PRESENCE OF COUNTER IONS USING REMARK 210 SANDER PROTOCOL. THE BACK REMARK 210 CALCULATIONS WERE PERFORMED REMARK 210 USING CORMA. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 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 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 1 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 DA A 3 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA A 7 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 7 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DC A 9 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT A 10 C6 - C5 - C7 ANGL. DEV. = -5.1 DEGREES REMARK 500 DA B 11 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 DA B 11 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA B 13 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT B 14 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 15 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 15 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG B 16 N1 - C6 - O6 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA B 17 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT B 18 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT B 20 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 DT B 20 C6 - C5 - C7 ANGL. DEV. = -5.6 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 DC A 9 0.06 SIDE_CHAIN REMARK 500 DG B 12 0.10 SIDE_CHAIN REMARK 500 DA B 13 0.10 SIDE_CHAIN REMARK 500 DG B 19 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MK6 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9- REMARK 900 HYDROXY-AFLATOXIN B1 ADDUCT MISPAIRED WITH DEOXYADENOSINE
DBREF 1MKL A 1 10 PDB 1MKL 1MKL 1 10 DBREF 1MKL B 11 20 PDB 1MKL 1MKL 11 20
SEQRES 1 A 10 DA DC DA DT DC X DA DT DC DT SEQRES 1 B 10 DA DG DA DT DC DG DA DT DG DT
MODRES 1MKL X A 6 DG
HET X A 6 70
HETNAM X 2'-DEOXY-N7-(8,9-DIHYDRO-9-HYDROXY-10-DEHYDROXY- HETNAM 2 X AFLATOXIN)GUANOSINE MONOPHOSPHATE
FORMUL 1 X C27 H27 N5 O14 P 1+
LINK O3' DC A 5 P X A 6 1555 1555 1.61 LINK O3' X A 6 P DA A 7 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