HEADER DNA 03-AUG-12 2LWM TITLE SOLUTION STRUCTURE OF DUPLEX DNA CONTAINING A B-CARBA-FAPY-DG LESION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*TP*AP*C*(LWM)P*CP*AP*TP*GP*C)-3'); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*CP*AP*TP*GP*CP*GP*TP*AP*CP*G)-3'); COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS OXIDATIVE DAMAGE, DNA EXPDTA SOLUTION NMR NUMMDL 26 MDLTYP MINIMIZED AVERAGE AUTHOR T.ZALIANYAK,C.DE LOS SANTOS,M.LUKIN,S.ATTALURI,F.JOHNSON REVDAT 1 20-FEB-13 2LWM 0 JRNL AUTH M.LUKIN,T.ZALIZNYAK,S.ATTALURI,F.JOHNSON,C.DE LOS SANTOS JRNL TITL SOLUTION STRUCTURE OF DUPLEX DNA CONTAINING A JRNL TITL 2 B-CARBA-FAPY-DG LESION JRNL REF CHEM.RES.TOXICOL. V. 25 2423 2012 JRNL REFN ISSN 0893-228X JRNL PMID 22897814 JRNL DOI 10.1021/TX300290B REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LWM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-13. REMARK 100 THE RCSB ID CODE IS RCSB102923. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 278 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.1 MM 11 MER DUPLEX OLIGO B-D, REMARK 210 25 MM PHOSPHATE BUFFER, 50 MM REMARK 210 NACL, 0.5 MM EDTA, 100% D2O; 1.1 REMARK 210 MM 11 MER DUPLEX OLIGO B-D, 25 MM REMARK 210 PHOSPHATE BUFFER, 50 MM NACL, 0.5 REMARK 210 MM EDTA, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY; REMARK 210 2D DQF-COSY; 2D 1H-1H TOCSY; 2D REMARK 210 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, SPARKY, X- REMARK 210 PLOR_NIH REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 25 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: B, D 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 B 3 C5 DT B 3 C7 0.038 REMARK 500 1 DT D 4 C5 DT D 4 C7 0.039 REMARK 500 2 DT B 9 C5 DT B 9 C7 0.036 REMARK 500 2 DT D 4 C5 DT D 4 C7 0.038 REMARK 500 2 DT D 8 C5 DT D 8 C7 0.036 REMARK 500 3 DT B 9 C5 DT B 9 C7 0.037 REMARK 500 3 DT D 4 C5 DT D 4 C7 0.038 REMARK 500 5 DT B 3 C5 DT B 3 C7 0.037 REMARK 500 5 DT D 4 C5 DT D 4 C7 0.038 REMARK 500 5 DT D 8 C5 DT D 8 C7 0.036 REMARK 500 6 DT B 3 C5 DT B 3 C7 0.041 REMARK 500 6 DA B 4 C4' DA B 4 C3' 0.066 REMARK 500 6 DT D 4 C5 DT D 4 C7 0.039 REMARK 500 7 DT B 3 C5 DT B 3 C7 0.042 REMARK 500 7 DT B 9 C5 DT B 9 C7 0.037 REMARK 500 7 DT D 4 C5 DT D 4 C7 0.039 REMARK 500 7 DT D 8 C5 DT D 8 C7 0.036 REMARK 500 8 DA B 4 C4' DA B 4 C3' 0.062 REMARK 500 8 DT D 4 C5 DT D 4 C7 0.037 REMARK 500 9 DT B 3 C5 DT B 3 C7 0.041 REMARK 500 9 DT D 4 C5 DT D 4 C7 0.036 REMARK 500 10 DT B 3 C5 DT B 3 C7 0.042 REMARK 500 10 DT D 4 C5 DT D 4 C7 0.037 REMARK 500 11 DT B 3 C5 DT B 3 C7 0.037 REMARK 500 11 DA B 4 C4' DA B 4 C3' 0.062 REMARK 500 11 DT D 4 C5 DT D 4 C7 0.037 REMARK 500 12 DT B 3 C5 DT B 3 C7 0.037 REMARK 500 12 DA B 4 C4' DA B 4 C3' 0.060 REMARK 500 13 DT B 3 C5 DT B 3 C7 0.036 REMARK 500 14 DT B 3 C5 DT B 3 C7 0.043 REMARK 500 14 DA B 4 C4' DA B 4 C3' 0.064 REMARK 500 14 DT D 4 C5 DT D 4 C7 0.037 REMARK 500 15 DT B 3 C5 DT B 3 C7 0.038 REMARK 500 15 DT B 9 C5 DT B 9 C7 0.038 REMARK 500 15 DT D 4 C5 DT D 4 C7 0.039 REMARK 500 16 DT B 3 C5 DT B 3 C7 0.040 REMARK 500 16 DT B 9 C5 DT B 9 C7 0.037 REMARK 500 16 DT D 4 C5 DT D 4 C7 0.038 REMARK 500 16 DT D 8 C5 DT D 8 C7 0.038 REMARK 500 17 DT B 3 C5 DT B 3 C7 0.042 REMARK 500 17 DA B 4 C4' DA B 4 C3' 0.061 REMARK 500 17 DT D 4 C5 DT D 4 C7 0.036 REMARK 500 18 DT B 3 C5 DT B 3 C7 0.037 REMARK 500 19 DT B 3 C5 DT B 3 C7 0.038 REMARK 500 19 DA B 4 C4' DA B 4 C3' 0.061 REMARK 500 19 DT B 9 C5 DT B 9 C7 0.036 REMARK 500 20 DT D 4 C5 DT D 4 C7 0.037 REMARK 500 21 DT B 3 C5 DT B 3 C7 0.040 REMARK 500 22 DT B 3 C5 DT B 3 C7 0.045 REMARK 500 22 DT B 9 C5 DT B 9 C7 0.041 REMARK 500 REMARK 500 THIS ENTRY HAS 60 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 DC B 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC B 5 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA D 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG D 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG D 7 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG D 11 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DC B 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG B 10 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DC B 11 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 DG D 1 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA D 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG D 5 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG D 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG D 11 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DC B 7 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DG D 5 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DG D 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DG D 11 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 4 DA D 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 4 DG D 5 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DG D 7 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 DG D 11 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 5 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 DC B 7 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 5 DG D 5 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 5 DG D 7 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 5 DG D 11 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 6 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 DC B 7 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 6 DT B 9 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 6 DC B 11 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 DG D 5 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 6 DG D 7 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 6 DC D 6 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 6 DG D 11 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 7 DA D 3 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 7 DG D 5 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 7 DC D 6 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 7 DG D 7 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 7 DC D 6 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 7 DG D 11 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 188 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18638 RELATED DB: BMRB REMARK 900 RELATED ID: 2LWN RELATED DB: PDB REMARK 900 RELATED ID: 2LWO RELATED DB: PDB DBREF 2LWM B 1 11 PDB 2LWM 2LWM 1 11 DBREF 2LWM D 1 11 PDB 2LWM 2LWM 1 11 SEQRES 1 B 11 DC DG DT DA DC LWM DC DA DT DG DC SEQRES 1 D 11 DG DC DA DT DG DC DG DT DA DC DG HET LWM B 6 38 HETNAM LWM [(1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-1,6- HETNAM 2 LWM DIHYDROPYRIMIDIN-4-YL]AMINO}-2- HETNAM 3 LWM HYDROXYCYCLOPENTYL]METHYL DIHYDROGEN PHOSPHATE FORMUL 1 LWM C11 H18 N5 O7 P LINK O3' DC B 5 P1 LWM B 6 1555 1555 1.62 LINK O3' LWM B 6 P DC B 7 1555 1555 1.63 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 217 0 1 0 0 0 0 6 0 0 0 2 END