PDB Short entry for 1DL4 HEADER DNA 08-DEC-99 1DL4 TITLE THE SOLUTION STRUCTURE OF A BAY-REGION 1S-BENZ[A]ANTHRACENE OXIDE TITLE 2 ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE TITLE 3 CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*GP*AP*CP*(BZA)AP*AP*GP*AP*AP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: BENZ[A]ANTHRACENE-MODIFIED ADENINE-6; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHESIZED BY CHEMICAL METHOD; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHESIZED BY CHEMICAL METHOD KEYWDS BENZ[A]ANTHRACENE-DNA DUPLEX, DNA EXPDTA SOLUTION NMR AUTHOR Z.LI,H.-Y.KIM,P.J.TAMURA,C.M.HARRIS,T.M.HARRIS,M.P.STONE REVDAT 5 16-FEB-22 1DL4 1 REMARK LINK REVDAT 4 24-FEB-09 1DL4 1 VERSN REVDAT 3 01-APR-03 1DL4 1 JRNL REVDAT 2 18-FEB-00 1DL4 1 REMARK HET LINK REVDAT 1 12-JAN-00 1DL4 0 JRNL AUTH Z.LI,H.Y.KIM,P.J.TAMURA,C.M.HARRIS,T.M.HARRIS,M.P.STONE JRNL TITL INTERCALATION OF THE JRNL TITL 2 (1S,2R,3S,4R)-N6-[1-(1,2,3,4-TETRAHYDRO-2,3, JRNL TITL 3 4-TRIHYDROXYBENZ[A]ANTHRACENYL)]-2'-DEOXYADENOSYL ADDUCT IN JRNL TITL 4 AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 JRNL TITL 5 SEQUENCE. JRNL REF BIOCHEMISTRY V. 38 16045 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10587427 JRNL DOI 10.1021/BI9903650 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.0, CORMA 5.2 REMARK 3 AUTHORS : BRUKER (XWINNMR), BORGIAS, B.A., THOMAS, P.D., LI, REMARK 3 H., KUMAR, A., AND TONELLI, M. (CORMA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF REMARK 3 477 NOE-DERIVED DISTANCE CONSTRAINTS, 80 EMPIRICAL SUGAR PUCKER REMARK 3 RESTRAINTS, 32 BACKBONE ANGLE DIHEDRAL RESTRAINTS, AND 18 REMARK 3 EMPIRICAL PLANARITY RESTRAINTS. REMARK 4 REMARK 4 1DL4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000010175. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 283; 298 REMARK 210 PH : 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 0.1 M NACL; 0.1 M NACL; 0.1 M REMARK 210 NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.7 MM OLIGODEOXYNUCLEOTIDE; 10 REMARK 210 MM PHOSPHATE BUFFER; 0.05 MM REMARK 210 EDTA; 0.1 M NACL; 1.7 MM REMARK 210 OLIGODEOXYNUCLEOTIDE; 10 MM REMARK 210 PHOSPHATE BUFFER; 0.05 MM EDTA; REMARK 210 0.1 M NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D ROESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.851, FELIX 97.0, REMARK 210 MARDIGRAS 3.0 REMARK 210 METHOD USED : NOE-RESTRAINTED MOLECULAR REMARK 210 DYNAMICS /SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 7 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES 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. = 2.1 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA A 4 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA A 6 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA A 7 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DA A 9 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA A 9 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA A 10 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA A 10 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG A 11 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT B 13 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT B 16 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DT B 17 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DG B 18 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG B 18 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG B 22 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 22 C8 - N9 - C4 ANGL. DEV. = -2.4 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 A 6 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BZA A 12 DBREF 1DL4 A 1 11 PDB 1DL4 1DL4 1 11 DBREF 1DL4 B 12 22 PDB 1DL4 1DL4 12 22 SEQRES 1 A 11 DC DG DG DA DC DA DA DG DA DA DG SEQRES 1 B 11 DC DT DT DC DT DT DG DT DC DC DG HET BZA A 12 36 HETNAM BZA 1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL FORMUL 3 BZA C18 H16 O3 LINK N6 DA A 6 C4C BZA A 12 1555 1555 1.34 SITE 1 AC1 6 DC A 5 DA A 6 DA A 7 DT B 16 SITE 2 AC1 6 DT B 17 DG B 18 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