Header list of 1mkl.pdb file
Complete list - 30 201 Bytes
HEADER DNA 29-AUG-02 1MKL
TITLE NMR REFINED STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-
TITLE 2 AFLATOXIN B1 ADDUCT IN A 5'-CPAFBG-3' SEQUENCE
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*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 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 STRUCTURE OF THE 8, 9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1
KEYWDS 2 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 3 30-JAN-19 1MKL 1 COMPND SOURCE REMARK DBREF
REVDAT 3 2 1 SEQRES HET HETNAM FORMUL
REVDAT 3 3 1 LINK ATOM
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) ADDUCT IN
JRNL TITL 3 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 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 3.0, X-PLOR 3.851
REMARK 3 AUTHORS : BRUKER (XWINNMR), A.T.BRUNGER (X-PLOR)
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. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-02.
REMARK 100 THE DEPOSITION ID IS D_1000016986.
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 0.1
REMARK 210 M NACL AND 0.05 MM NA2EDTA AT PD
REMARK 210 7.2, IN 99.999% D2O; 0.5 ML OF
REMARK 210 0.01 M SODIUM PHOSPHATE BUFFER
REMARK 210 CONTAINING 0.1 M NACL AND 0.05
REMARK 210 MM NA2EDTA AT PH 7.2, IN 9:1 H2O:
REMARK 210 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 : FELIX 97, MARDIGRAS 5.2, CORMA
REMARK 210 5.2, AMBER 6.0
REMARK 210 METHOD USED : DATA WAS PROCESSED USING FELIX
REMARK 210 97. THE NOE INTENSITIES WERE
REMARK 210 CONVERTED TO DISTANCE USING
REMARK 210 RANMARDI MODULE OF MARDIGRAS.
REMARK 210 STARTING STRUCTURES WERE BUILT
REMARK 210 USING INSIGHTII. XPLOR WAS USED
REMARK 210 FOR STRUCTURAL REFINEMENT. FINAL
REMARK 210 AVERAGED STRUCTURE WAS SOLVATED
REMARK 210 USING 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 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 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 DG A 6 0.15 SIDE CHAIN
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-HYDROXY-
REMARK 900 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 DG DA DT DC DT
SEQRES 1 B 10 DA DG DA DT DC 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 1.50
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
Complete list - 30 201 Bytes