HEADER DNA 29-DEC-00 1HT7 TITLE STRUCTURE OF A DNA DUPLEX CONTAINING A BISTRAND ABASIC SITE LESION TITLE 2 STAGGERED IN A 5'-ORIENTATION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*AP*TP*GP*(3DR)P*GP*TP*AP*CP*GP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: MODIFIED DNA DUPLEX CONTAINING CLUSTERED ABASIC SITES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*GP*CP*GP*TP*AP*(3DR)P*AP*CP*AP*TP*GP*CP*G)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RANDOMLY DESIGNED SEQUENCE CONTAINING STABLE ABASIC SOURCE 4 SITES (3DR).; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: RANDOMLY DESIGNED SEQUENCE CONTAINING STABLE ABASIC SOURCE 8 SITES (3DR). KEYWDS DOUBLE HELIX, ABASIC SITES, CLUSTERED DAMAGE, EXTRUDED RESIDUES., DNA EXPDTA SOLUTION NMR NUMMDL 6 AUTHOR Z.LIN,C.DE LOS SANTOS REVDAT 4 22-MAY-24 1HT7 1 REMARK REVDAT 3 23-FEB-22 1HT7 1 REMARK LINK REVDAT 2 24-FEB-09 1HT7 1 VERSN REVDAT 1 02-MAY-01 1HT7 0 JRNL AUTH Z.LIN,C.DE LOS SANTOS JRNL TITL NMR CHARACTERIZATION OF CLUSTERED BISTRAND ABASIC SITE JRNL TITL 2 LESIONS: EFFECT OF ORIENTATION ON THEIR SOLUTION STRUCTURE. JRNL REF J.MOL.BIOL. V. 308 341 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11327771 JRNL DOI 10.1006/JMBI.2001.4587 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 98, X-PLOR 3.1 REMARK 3 AUTHORS : MSI (FELIX), A. BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1) HEATING STAGE: FROM 100 TO 500 K IN REMARK 3 4PS. INTRODUCTION OF EXPERIMENTAL RESTRAINTS AT THE END OF THIS REMARK 3 STAGE. 2) HIGH TEMPERATURE STAGE: 80 PS DYNAMICS AT 500K 3) REMARK 3 COOLING STAGE: FROM 500 TO 300K IN 40PS. 4) EQUILIBRATION STAGE: REMARK 3 140PS DYNAMICS AT 300K. REMARK 4 REMARK 4 1HT7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-01. REMARK 100 THE DEPOSITION ID IS D_1000012572. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 276 REMARK 210 PH : 7.6; 7.6 REMARK 210 IONIC STRENGTH : NOT DETERMINED; NOT DETERMINED REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM DUPLEX IN 20 MM PHOSPHATE REMARK 210 BUFFER, PH 7.6; 50 MM NACL; 1 MM REMARK 210 EDTA.; 2MM DUPLEX IN 20 MM REMARK 210 PHOSPHATE BUFFER, PH 7.6; 50 MM REMARK 210 NACL; 1 MM EDTA. REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; COSY, COSY45, TOCSY, REMARK 210 DQFCOSY, HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MARDIGRAS 5, INSIGHT 95, MIDAS REMARK 210 PLUS, CURVES 5 REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 6 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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: 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 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 DC A 1 C4 DC A 1 N4 0.094 REMARK 500 1 DG A 2 C2 DG A 2 N2 0.083 REMARK 500 1 DC A 3 C4 DC A 3 N4 0.093 REMARK 500 1 DA A 4 C6 DA A 4 N6 0.093 REMARK 500 1 DT A 5 C5 DT A 5 C7 0.037 REMARK 500 1 DG A 6 C2 DG A 6 N2 0.086 REMARK 500 1 DG A 8 C2 DG A 8 N2 0.078 REMARK 500 1 DT A 9 C5 DT A 9 C7 0.036 REMARK 500 1 DA A 10 C6 DA A 10 N6 0.092 REMARK 500 1 DC A 11 C4 DC A 11 N4 0.096 REMARK 500 1 DG A 12 C2 DG A 12 N2 0.084 REMARK 500 1 DC A 13 C4 DC A 13 N4 0.093 REMARK 500 1 DG B 14 C2 DG B 14 N2 0.081 REMARK 500 1 DC B 15 C4 DC B 15 N4 0.093 REMARK 500 1 DG B 16 C2 DG B 16 N2 0.080 REMARK 500 1 DA B 18 C6 DA B 18 N6 0.096 REMARK 500 1 DA B 20 C6 DA B 20 N6 0.094 REMARK 500 1 DC B 21 C4 DC B 21 N4 0.094 REMARK 500 1 DA B 22 C6 DA B 22 N6 0.092 REMARK 500 1 DT B 23 C5 DT B 23 C7 0.038 REMARK 500 1 DG B 24 C2 DG B 24 N2 0.084 REMARK 500 1 DC B 25 C4 DC B 25 N4 0.093 REMARK 500 1 DG B 26 C2 DG B 26 N2 0.085 REMARK 500 2 DC A 1 C4 DC A 1 N4 0.095 REMARK 500 2 DG A 2 C2 DG A 2 N2 0.081 REMARK 500 2 DC A 3 C4 DC A 3 N4 0.093 REMARK 500 2 DA A 4 C6 DA A 4 N6 0.094 REMARK 500 2 DT A 5 C5 DT A 5 C7 0.036 REMARK 500 2 DG A 6 C2 DG A 6 N2 0.085 REMARK 500 2 DG A 8 C2 DG A 8 N2 0.078 REMARK 500 2 DT A 9 C5 DT A 9 C7 0.038 REMARK 500 2 DA A 10 C6 DA A 10 N6 0.092 REMARK 500 2 DC A 11 C4 DC A 11 N4 0.098 REMARK 500 2 DG A 12 C2 DG A 12 N2 0.083 REMARK 500 2 DC A 13 C4 DC A 13 N4 0.093 REMARK 500 2 DG B 14 C2 DG B 14 N2 0.079 REMARK 500 2 DC B 15 C4 DC B 15 N4 0.092 REMARK 500 2 DG B 16 C2 DG B 16 N2 0.080 REMARK 500 2 DA B 18 C6 DA B 18 N6 0.095 REMARK 500 2 DA B 20 C6 DA B 20 N6 0.096 REMARK 500 2 DC B 21 C4 DC B 21 N4 0.095 REMARK 500 2 DA B 22 C6 DA B 22 N6 0.095 REMARK 500 2 DT B 23 C5 DT B 23 C7 0.038 REMARK 500 2 DG B 24 C2 DG B 24 N2 0.084 REMARK 500 2 DC B 25 C4 DC B 25 N4 0.095 REMARK 500 2 DG B 26 C2 DG B 26 N2 0.084 REMARK 500 3 DC A 1 C4 DC A 1 N4 0.093 REMARK 500 3 DG A 2 C2 DG A 2 N2 0.083 REMARK 500 3 DC A 3 C4 DC A 3 N4 0.094 REMARK 500 3 DA A 4 C6 DA A 4 N6 0.093 REMARK 500 REMARK 500 THIS ENTRY HAS 137 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 DG A 2 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 6 C3' - C2' - C1' ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 6 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 10 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 10 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DC A 11 C4' - C3' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 11.8 DEGREES REMARK 500 1 DG A 12 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DC A 13 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DG B 14 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DC B 15 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA B 20 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT B 23 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG B 24 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DC B 25 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG A 2 C1' - O4' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 2 DG A 2 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DG A 6 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DG A 8 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DA A 10 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DA A 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 DC A 11 C4' - C3' - C2' ANGL. DEV. = -6.2 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 11.8 DEGREES REMARK 500 2 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DG A 12 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DC A 13 O4' - C1' - N1 ANGL. DEV. = 8.2 DEGREES REMARK 500 2 DG B 14 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DC B 15 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 DT B 17 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DA B 20 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC B 21 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DC B 21 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DG B 24 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DG B 26 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DG A 2 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 3 DG A 2 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 3 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DG A 6 C3' - C2' - C1' ANGL. DEV. = -6.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 135 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HT4 RELATED DB: PDB REMARK 900 STRUCTURE OF A DNA DUPLEX CONTAINING A BISTRAND ABASIC SITE LESION REMARK 900 STAGGERED IN A 3'-ORIENTATION DBREF 1HT7 A 1 13 PDB 1HT7 1HT7 1 13 DBREF 1HT7 B 14 26 PDB 1HT7 1HT7 14 26 SEQRES 1 A 13 DC DG DC DA DT DG 3DR DG DT DA DC DG DC SEQRES 1 B 13 DG DC DG DT DA 3DR DA DC DA DT DG DC DG HET 3DR A 7 19 HET 3DR B 19 19 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 1 3DR 2(C5 H11 O6 P) LINK O3' DG A 6 P 3DR A 7 1555 1555 1.62 LINK O3' 3DR A 7 P DG A 8 1555 1555 1.62 LINK O3' DA B 18 P 3DR B 19 1555 1555 1.62 LINK O3' 3DR B 19 P DA B 20 1555 1555 1.62 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