HEADER DNA 10-OCT-01 1K5E TITLE SOLUTION STRUCTURE OF R-STYRENE ADDUCT IN THE RAS61 SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*GP*AP*CP*(ABR)P*AP*GP*AP*AP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: N-RAS PROTOONCOGENE; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: N-RAS PROTOONCOGENE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS GENERATED BY AN OLIGONUCLEOTIDE SOURCE 4 SYNTHESIZER; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: THIS SEQUENCE WAS GENERATED BY AN OLIGONUCLEOTIDE SOURCE 8 SYNTHESIZER KEYWDS STYRENE, DNA ADDUCT, SOLUTION STRUCTURE OF DNA, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR C.HENNARD,J.FINNEMAN,C.M.HARRIS,T.M.HARRIS,M.P.STONE REVDAT 3 23-FEB-22 1K5E 1 REMARK LINK REVDAT 2 24-FEB-09 1K5E 1 VERSN REVDAT 1 23-JAN-02 1K5E 0 JRNL AUTH C.HENNARD,J.FINNEMAN,C.M.HARRIS,T.M.HARRIS,M.P.STONE JRNL TITL THE NONMUTAGENIC (R)- AND (S)-BETA-(N(6)-ADENYL)STYRENE JRNL TITL 2 OXIDE ADDUCTS ARE ORIENTED IN THE MAJOR GROOVE AND SHOW JRNL TITL 3 LITTLE PERTURBATION TO DNA STRUCTURE. JRNL REF BIOCHEMISTRY V. 40 9780 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11502171 JRNL DOI 10.1021/BI010564V REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 97, MARDIGRAS 3.0 REMARK 3 AUTHORS : MOLECULAR SIMULATIONS (FELIX), JAMES, TL REMARK 3 (MARDIGRAS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1K5E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1000014581. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 10MM PHOSPHATE BUFFER REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 130 OD260 OF DOUBLE STRANDED REMARK 210 OLIGODEOXYNUCLEOTIDE ARE REMARK 210 DISSOLVED IN 0.5 ML NMR BUFFER REMARK 210 CONTAINING 99.996% D2O. REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.85, CORMA 4.0 REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS, MATRIX RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NOESY AT 100, 150 AND 200 MS MIXING TIME 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HA ABR A 6 O4 DT B 16 1.43 REMARK 500 H2'' DC B 15 O5' DT B 16 1.48 REMARK 500 CA ABR A 6 O4 DT B 16 2.15 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.8 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 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA A 7 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DA A 9 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 10 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA A 10 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 11 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT B 13 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT B 17 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG B 18 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG B 18 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG B 22 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG B 22 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K5F RELATED DB: PDB REMARK 900 1K5F IS THE SAME STRUCTURE WITH (S)-(N-PHENYL-2-HYDROXY-ETHYL)-2'- REMARK 900 DEOXY-ADENOSINE-5'-MONOPHOSPHATE. DBREF 1K5E A 1 11 PDB 1K5E 1K5E 1 11 DBREF 1K5E B 12 22 PDB 1K5E 1K5E 12 22 SEQRES 1 A 11 DC DG DG DA DC ABR DA DG DA DA DG SEQRES 1 B 11 DC DT DT DC DT DT DG DT DC DC DG MODRES 1K5E ABR A 6 DA HET ABR A 6 49 HETNAM ABR (R)-(N-PHENYL-2-HYDROXY-ETHYL)-2'-DEOXY-ADENOSINE-5'- HETNAM 2 ABR MONOPHOSPHATE FORMUL 1 ABR C18 H22 N5 O7 P LINK O3' DC A 5 P ABR A 6 1555 1555 1.61 LINK O3' ABR A 6 P DA A 7 1555 1555 1.61 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