HEADER DNA 12-JAN-04 1S37 TITLE ACCOMODATION OF MISPAIR-ALIGNED N3T-ETHYL-N3T DNA INTERSTRAND TITLE 2 CROSSLINK COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*AP*AP*AP*(TTM)P*TP*TP*TP*CP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*GP*AP*AP*AP*TP*TP*TP*TP*CP*G)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS INTERSTRAND CROSSLINK, DNA INTERSTRAND CROSS-LINK, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR M.W.DA SILVA,A.M.NORONHA,D.M.NOLL,P.S.MILLER,O.M.COLVIN,M.P.GAMCSIK REVDAT 3 30-JUL-14 1S37 1 ATOM DBREF SEQRES VERSN REVDAT 2 24-FEB-09 1S37 1 VERSN REVDAT 1 25-JAN-05 1S37 0 JRNL AUTH M.W.DA SILVA,C.J.WILDS,A.M.NORONHA,O.M.COLVIN,P.S.MILLER, JRNL AUTH 2 M.P.GAMCSIK JRNL TITL ACCOMMODATION OF MISPAIR ALIGNED N3T-ETHYL-N3T DNA JRNL TITL 2 INTERSTRAND CROSS LINK. JRNL REF BIOCHEMISTRY V. 43 12549 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15449944 JRNL DOI 10.1021/BI0486435 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.2 REMARK 3 AUTHORS : A.T. BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1S37 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-04. REMARK 100 THE RCSB ID CODE IS RCSB021309. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273; 298 REMARK 210 PH : 7.4; 7.4 REMARK 210 IONIC STRENGTH : 0.1 MM NACL; 0.1 MM NACL REMARK 210 PRESSURE : NORMAL; NORMAL REMARK 210 SAMPLE CONTENTS : 100 MM NACL, PH 7.4 ADJUSTED REMARK 210 WITH PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 8 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 8 REMARK 210 REMARK 210 REMARK: STRUCTURE DETERMINED USING STANDARD NMR EXPERIMENTS. 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' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 DG A 2 C3' - C2' - C1' ANGL. DEV. = -7.7 DEGREES REMARK 500 DG A 2 O4' - C1' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 DA A 3 O4' - C1' - C2' ANGL. DEV. = -7.9 DEGREES REMARK 500 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA A 3 C6 - N1 - C2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA A 3 N1 - C6 - N6 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA A 4 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA A 5 C4' - C3' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 DA A 5 N1 - C6 - N6 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT A 7 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT A 7 O4' - C1' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 DT A 7 C4 - C5 - C6 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT A 7 C4 - C5 - C7 ANGL. DEV. = 3.6 DEGREES REMARK 500 DT A 7 C6 - C5 - C7 ANGL. DEV. = -7.3 DEGREES REMARK 500 DT A 8 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT A 8 C4 - C5 - C6 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DT A 9 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 DT A 9 O4' - C1' - C2' ANGL. DEV. = -10.3 DEGREES REMARK 500 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT A 9 C4 - C5 - C6 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT A 9 C6 - C5 - C7 ANGL. DEV. = -6.9 DEGREES REMARK 500 DC A 10 C3' - C2' - C1' ANGL. DEV. = -8.0 DEGREES REMARK 500 DC A 10 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC A 10 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG A 11 O4' - C4' - C3' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC B 1 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 DC B 1 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 DG B 2 C3' - C2' - C1' ANGL. DEV. = -7.5 DEGREES REMARK 500 DG B 2 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 DA B 3 O4' - C1' - C2' ANGL. DEV. = -8.0 DEGREES REMARK 500 DA B 3 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA B 3 C6 - N1 - C2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA B 3 N1 - C6 - N6 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA B 4 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 DA B 4 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 DA B 4 N1 - C6 - N6 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA B 5 C4' - C3' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 DA B 5 N1 - C6 - N6 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT B 6 C6 - C5 - C7 ANGL. DEV. = -6.4 DEGREES REMARK 500 DT B 7 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT B 7 O4' - C1' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 DT B 7 C4 - C5 - C6 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT B 7 C6 - C5 - C7 ANGL. DEV. = -6.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 63 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 DT A 9 -45.7 D D OUTSIDE RANGE REMARK 500 DT B 9 -45.8 D D OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1N74 RELATED DB: PDB REMARK 900 DNA INTERSTRAND CROSSLINK REMARK 900 RELATED ID: 1N4B RELATED DB: PDB REMARK 900 DNA INTERSTRAND CROSSLINK DBREF 1S37 A 1 11 PDB 1S37 1S37 1 11 DBREF 1S37 B 1 11 PDB 1S37 1S37 1 11 SEQRES 1 A 11 DC DG DA DA DA TTM DT DT DT DC DG SEQRES 1 B 11 DC DG DA DA DA DT DT DT DT DC DG MODRES 1S37 TTM A 6 DT N3-ETHYL-THYMIDINE-5'-MONOPHOSPHATE HET TTM A 6 37 HETNAM TTM N3-ETHYL-THYMIDINE-5'-MONOPHOSPHATE FORMUL 1 TTM C12 H19 N2 O8 P LINK O3' DA A 5 P TTM A 6 1555 1555 1.59 LINK O3' TTM A 6 P DT A 7 1555 1555 1.59 LINK C2Q TTM A 6 N3 DT B 6 1555 1555 1.48 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 MASTER 160 0 1 0 0 0 0 6 0 0 0 2 END