HEADER DNA 22-JUL-97 1SJK TITLE A DUPLEX DNA WITH AN ABASIC SITE IN A DA TRACT, ALPHA FORM, TITLE 2 NMR, MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*AP*AP*AP*AP*AP*TP*GP*CP*G)- COMPND 3 3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*CP*GP*CP*AP*TP*TP*ORPP*TP*TP*GP*CP*G)- COMPND 8 3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DUPLEX DNA WITH AN ABASIC SITE IN A DA TRACT, DAMAGED DNA, KEYWDS 2 AT TRACT DNA, DEOXYRIBONUCLEIC ACID EXPDTA SOLUTION NMR AUTHOR K.Y.WANG,S.A.PARKER,I.GOLJER,P.H.BOLTON REVDAT 2 24-FEB-09 1SJK 1 VERSN REVDAT 1 03-DEC-97 1SJK 0 JRNL AUTH K.Y.WANG,S.A.PARKER,I.GOLJER,P.H.BOLTON JRNL TITL SOLUTION STRUCTURE OF A DUPLEX DNA WITH AN ABASIC JRNL TITL 2 SITE IN A DA TRACT. JRNL REF BIOCHEMISTRY V. 36 11629 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9305952 JRNL DOI 10.1021/BI971464L REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SJK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 6 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS IS THE AVERAGE OF SIX STRUCTURES CALCULATED AT 2PS REMARK 210 INTERVALS FROM 70 PICOSECONDS TO 80 PICOSECONDS DURING REMARK 210 RESTRAINED MOLECULAR DYNAMICS. 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 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 DC A 1 O5' DC A 1 C5' -0.361 REMARK 500 DG A 2 P DG A 2 OP2 -0.115 REMARK 500 DA A 5 P DA A 5 OP1 -0.185 REMARK 500 DA A 5 P DA A 5 OP2 -0.178 REMARK 500 DA A 5 P DA A 5 O5' -0.083 REMARK 500 DA A 6 O3' DA A 6 C3' -0.049 REMARK 500 DA A 7 P DA A 7 OP2 -0.141 REMARK 500 DA A 7 O5' DA A 7 C5' -0.325 REMARK 500 DA A 7 C4' DA A 7 C3' -0.069 REMARK 500 DA A 7 O3' DA A 7 C3' -0.036 REMARK 500 DA A 6 O3' DA A 7 P -0.166 REMARK 500 DA A 8 P DA A 8 OP1 -0.334 REMARK 500 DA A 8 P DA A 8 OP2 -0.388 REMARK 500 DA A 8 P DA A 8 O5' -0.332 REMARK 500 DA A 8 O5' DA A 8 C5' -0.300 REMARK 500 DA A 8 C5' DA A 8 C4' -0.099 REMARK 500 DA A 8 C4' DA A 8 C3' -0.076 REMARK 500 DT A 9 P DT A 9 O5' -0.062 REMARK 500 DT A 9 N3 DT A 9 C4 -0.056 REMARK 500 DT B 17 C5 DT B 17 C7 0.055 REMARK 500 DT B 20 C5 DT B 20 C7 0.046 REMARK 500 DT B 21 P DT B 21 O5' -0.099 REMARK 500 DT B 21 C5 DT B 21 C7 0.047 REMARK 500 DG B 22 P DG B 22 OP1 -0.118 REMARK 500 DG B 22 P DG B 22 OP2 -0.132 REMARK 500 DG B 22 P DG B 22 O5' -0.101 REMARK 500 DG B 24 C3' DG B 24 C2' -0.067 REMARK 500 DG B 24 C6 DG B 24 N1 -0.046 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 DG A 2 P - O5' - C5' ANGL. DEV. = 12.9 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG A 2 C3' - O3' - P ANGL. DEV. = 10.9 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA A 5 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DA A 4 C3' - O3' - P ANGL. DEV. = 9.5 DEGREES REMARK 500 DA A 6 P - O5' - C5' ANGL. DEV. = 12.4 DEGREES REMARK 500 DA A 6 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA A 5 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DA A 7 O5' - C5' - C4' ANGL. DEV. = 35.3 DEGREES REMARK 500 DA A 7 P - O5' - C5' ANGL. DEV. = 18.2 DEGREES REMARK 500 DA A 7 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 6 C3' - O3' - P ANGL. DEV. = 29.1 DEGREES REMARK 500 DA A 8 O5' - P - OP1 ANGL. DEV. = -6.2 DEGREES REMARK 500 DA A 8 O5' - C5' - C4' ANGL. DEV. = 28.6 DEGREES REMARK 500 DA A 8 P - O5' - C5' ANGL. DEV. = 15.0 DEGREES REMARK 500 DA A 8 O4' - C4' - C3' ANGL. DEV. = 8.2 DEGREES REMARK 500 DA A 8 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 DT A 9 P - O5' - C5' ANGL. DEV. = 10.1 DEGREES REMARK 500 DT A 9 C5 - C6 - N1 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA A 8 C3' - O3' - P ANGL. DEV. = 12.6 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC A 11 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC A 11 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG A 10 C3' - O3' - P ANGL. DEV. = 10.6 DEGREES REMARK 500 DG A 12 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 11 C3' - O3' - P ANGL. DEV. = 12.2 DEGREES REMARK 500 DC B 13 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC B 13 C2 - N3 - C4 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC B 13 N1 - C2 - O2 ANGL. DEV. = 5.1 DEGREES REMARK 500 DG B 14 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 DG B 14 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 DA B 16 P - O5' - C5' ANGL. DEV. = 10.4 DEGREES REMARK 500 DA B 16 O4' - C1' - N9 ANGL. DEV. = 6.8 DEGREES REMARK 500 DA B 16 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT B 17 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 DA B 16 C3' - O3' - P ANGL. DEV. = 9.1 DEGREES REMARK 500 DT B 18 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT B 18 C6 - C5 - C7 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT B 20 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT B 20 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DT B 21 P - O5' - C5' ANGL. DEV. = 14.7 DEGREES REMARK 500 DT B 21 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT B 21 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 56 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SJL RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE DBREF 1SJK A 1 12 PDB 1SJK 1SJK 1 12 DBREF 1SJK B 13 24 PDB 1SJK 1SJK 13 24 SEQRES 1 A 12 DC DG DC DA DA DA DA DA DT DG DC DG SEQRES 1 B 12 DC DG DC DA DT DT ORP DT DT DG DC DG HET ORP B 19 20 HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE FORMUL 2 ORP C5 H11 O7 P LINK O3 ORP B 19 P DT B 20 1555 1555 1.59 LINK P ORP B 19 O3' DT B 18 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 MASTER 166 0 1 0 0 0 0 6 0 0 0 2 END