HEADER DNA 28-JUL-11 2LGM TITLE STRUCTURE OF DNA CONTAINING AN ARISTOLACTAM II-DA LESION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*TP*AP*CP*AP*CP*AP*TP*GP*C)-3'); COMPND 3 CHAIN: 1; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*CP*AP*TP*GP*TP*GP*TP*AP*CP*G)-3'); COMPND 7 CHAIN: 2; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DUPLEX STABILITY, NER RECOGNITION, DNA EXPDTA SOLUTION NMR NUMMDL 26 MDLTYP MINIMIZED AVERAGE AUTHOR M.LUKIN,T.ZALIZNYAK,F.JOHNSON,C.DE LOS SANTOS REVDAT 3 14-JUN-23 2LGM 1 REMARK LINK REVDAT 2 11-APR-12 2LGM 1 JRNL REVDAT 1 30-NOV-11 2LGM 0 JRNL AUTH M.LUKIN,T.ZALIZNYAK,F.JOHNSON,C.DE LOS SANTOS JRNL TITL STRUCTURE AND STABILITY OF DNA CONTAINING AN ARISTOLACTAM JRNL TITL 2 II-DA LESION: IMPLICATIONS FOR THE NER RECOGNITION OF BULKY JRNL TITL 3 ADDUCTS. JRNL REF NUCLEIC ACIDS RES. V. 40 2759 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22121223 JRNL DOI 10.1093/NAR/GKR1094 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LGM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000102368. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300; 278 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.25 MM DNA 11M DUPL ALII, 25 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 100% D2O; 0.25 MM DNA REMARK 210 11M DUPL ALII, 25 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H COSY; 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY, HYPER, VNMR, REMARK 210 TOPSPIN REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 26 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 26 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: 1, 2 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 DT 1 9 C5 DT 1 9 C7 0.037 REMARK 500 1 DT 2 8 C5 DT 2 8 C7 0.039 REMARK 500 2 DT 1 9 C5 DT 1 9 C7 0.039 REMARK 500 2 DT 2 8 C5 DT 2 8 C7 0.040 REMARK 500 3 DT 1 9 C5 DT 1 9 C7 0.040 REMARK 500 3 DT 2 4 C5 DT 2 4 C7 0.039 REMARK 500 3 DT 2 8 C5 DT 2 8 C7 0.040 REMARK 500 4 DT 2 6 C5 DT 2 6 C7 0.040 REMARK 500 4 DT 2 8 C5 DT 2 8 C7 0.037 REMARK 500 5 DT 1 9 C5 DT 1 9 C7 0.039 REMARK 500 5 DT 2 4 C5 DT 2 4 C7 0.036 REMARK 500 5 DT 2 6 C5 DT 2 6 C7 0.036 REMARK 500 5 DT 2 8 C5 DT 2 8 C7 0.040 REMARK 500 6 DT 1 9 C5 DT 1 9 C7 0.042 REMARK 500 6 DT 2 6 C5 DT 2 6 C7 0.037 REMARK 500 6 DT 2 8 C5 DT 2 8 C7 0.041 REMARK 500 7 DT 1 9 C5 DT 1 9 C7 0.040 REMARK 500 7 DT 2 4 C5 DT 2 4 C7 0.037 REMARK 500 7 DT 2 6 C5 DT 2 6 C7 0.038 REMARK 500 7 DT 2 8 C5 DT 2 8 C7 0.040 REMARK 500 8 DT 1 9 C5 DT 1 9 C7 0.040 REMARK 500 8 DT 2 6 C5 DT 2 6 C7 0.038 REMARK 500 8 DT 2 8 C5 DT 2 8 C7 0.042 REMARK 500 9 DT 2 6 C5 DT 2 6 C7 0.038 REMARK 500 9 DT 2 8 C5 DT 2 8 C7 0.037 REMARK 500 10 DT 2 6 C5 DT 2 6 C7 0.040 REMARK 500 11 DT 2 6 C5 DT 2 6 C7 0.042 REMARK 500 11 DT 2 8 C5 DT 2 8 C7 0.037 REMARK 500 12 DT 2 6 C5 DT 2 6 C7 0.039 REMARK 500 13 DT 2 6 C5 DT 2 6 C7 0.040 REMARK 500 13 DT 2 8 C5 DT 2 8 C7 0.038 REMARK 500 14 DT 1 9 C5 DT 1 9 C7 0.039 REMARK 500 14 DT 2 4 C5 DT 2 4 C7 0.037 REMARK 500 14 DT 2 6 C5 DT 2 6 C7 0.037 REMARK 500 14 DT 2 8 C5 DT 2 8 C7 0.041 REMARK 500 15 DT 1 3 C5 DT 1 3 C7 0.037 REMARK 500 15 DT 1 9 C5 DT 1 9 C7 0.040 REMARK 500 15 DT 2 4 C5 DT 2 4 C7 0.037 REMARK 500 15 DT 2 6 C5 DT 2 6 C7 0.041 REMARK 500 15 DT 2 8 C5 DT 2 8 C7 0.042 REMARK 500 16 DT 1 3 C5 DT 1 3 C7 0.038 REMARK 500 16 DT 1 9 C5 DT 1 9 C7 0.039 REMARK 500 16 DT 2 4 C5 DT 2 4 C7 0.037 REMARK 500 16 DT 2 8 C5 DT 2 8 C7 0.041 REMARK 500 17 DT 2 6 C5 DT 2 6 C7 0.039 REMARK 500 17 DT 2 8 C5 DT 2 8 C7 0.036 REMARK 500 18 DT 1 3 C5 DT 1 3 C7 0.039 REMARK 500 18 DT 1 9 C5 DT 1 9 C7 0.042 REMARK 500 18 DT 2 4 C5 DT 2 4 C7 0.036 REMARK 500 18 DT 2 8 C5 DT 2 8 C7 0.041 REMARK 500 REMARK 500 THIS ENTRY HAS 70 BOND DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL 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 1 DT 1 3 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DA 1 4 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DA 1 6 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA 1 6 N1 - C6 - N6 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DA 1 6 C5 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC 1 7 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DC 1 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT 1 9 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG 1 10 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DC 1 11 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG 2 1 O5' - C5' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DC 2 2 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT 2 6 O4' - C1' - N1 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DT 2 6 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG 2 7 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC 2 10 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC 1 1 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 2 DT 1 3 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 2 DA 1 4 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA 1 6 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DA 1 6 N1 - C6 - N6 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 DA 1 6 C5 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DC 1 7 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DC 1 7 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC 1 7 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DT 1 9 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DC 1 11 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DG 2 1 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DC 2 2 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT 2 6 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DT 2 6 O4' - C1' - N1 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DT 2 6 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT 2 6 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 2 DG 2 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DT 1 3 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 3 DA 1 4 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 3 DA 1 4 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 DA 1 6 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DA 1 6 N1 - C6 - N6 ANGL. DEV. = 6.0 DEGREES REMARK 500 3 DA 1 6 C5 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 3 DC 1 7 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 3 DC 1 7 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DT 1 9 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 DG 1 10 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 3 DC 1 11 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DG 2 1 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DC 2 2 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DT 2 4 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 3 DT 2 6 O4' - C1' - N1 ANGL. DEV. = -5.5 DEGREES REMARK 500 3 DT 2 6 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 388 ANGLE DEVIATIONS. 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 A4A 1 12 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17814 RELATED DB: BMRB DBREF 2LGM 1 1 11 PDB 2LGM 2LGM 1 11 DBREF 2LGM 2 1 11 PDB 2LGM 2LGM 1 11 SEQRES 1 1 11 DC DG DT DA DC DA DC DA DT DG DC SEQRES 1 2 11 DG DC DA DT DG DT DG DT DA DC DG HET A4A 1 12 28 HETNAM A4A [1,3]BENZODIOXOLO[6,5,4-CD]BENZO[F]INDOL-5(6H)-ONE HETSYN A4A ARISTOLACTAM II FORMUL 3 A4A C16 H9 N O3 LINK N6 DA 1 6 C7 A4A 1 12 1555 1555 1.51 SITE 1 AC1 5 DC 1 5 DA 1 6 DG 2 5 DT 2 6 SITE 2 AC1 5 DG 2 7 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 MODEL 1