Header list of 1mk6.pdb file
Complete list - 30 201 Bytes
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
Complete list - 30 201 Bytes