HEADER DNA 03-OCT-00 1FZL TITLE DNA WITH PYRENE PAIRED AT ABASIC SITES COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*AP*CP*AP*AP*AP*CP*AP*(PYP)P*GP*CP*AP*C)- COMPND 3 3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*GP*TP*GP*CP*(3DR)P*TP*GP*TP*TP*TP*GP*TP*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 PYRENE, TETRAHYDROFURAN, NON-HYDROGEN BONDED DNA BASE PAIR EXPDTA SOLUTION NMR NUMMDL 6 AUTHOR S.SMIRNOV,T.J.MATRAY,E.T.KOOL,C.DE LOS SANTOS REVDAT 3 24-FEB-09 1FZL 1 VERSN REVDAT 2 07-JAN-03 1FZL 1 JRNL REMARK MASTER REVDAT 1 18-OCT-00 1FZL 0 JRNL AUTH S.SMIRNOV,T.J.MATRAY,E.T.KOOL,C.DE LOS SANTOS JRNL TITL INTEGRITY OF DUPLEX STRUCTURES WITHOUT HYDROGEN JRNL TITL 2 BONDING: DNA WITH PYRENE PAIRED AT ABASIC SITES JRNL REF NUCLEIC ACIDS RES. V. 30 5561 2002 JRNL REFN ISSN 0305-1048 JRNL PMID 12490724 JRNL DOI 10.1093/NAR/GKF688 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : A. BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FZL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-00. REMARK 100 THE RCSB ID CODE IS RCSB012047. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 284; 308 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 50 MM; 50 MM REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 3.6 MM; 3.6 MM REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 5, FELIX 95 REMARK 210 METHOD USED : MOLECULAR ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 15 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 6 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 3 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-6 REMARK 470 RES CSSEQI ATOMS REMARK 470 PYP A 9 O3P 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 0.095 REMARK 500 1 DA A 2 C6 DA A 2 N6 0.089 REMARK 500 1 DC A 3 C4 DC A 3 N4 0.095 REMARK 500 1 DA A 4 C6 DA A 4 N6 0.095 REMARK 500 1 DA A 5 C6 DA A 5 N6 0.096 REMARK 500 1 DA A 6 C6 DA A 6 N6 0.095 REMARK 500 1 DC A 7 C4 DC A 7 N4 0.095 REMARK 500 1 DA A 8 C6 DA A 8 N6 0.097 REMARK 500 1 DG A 10 C2 DG A 10 N2 0.083 REMARK 500 1 DC A 11 C4 DC A 11 N4 0.095 REMARK 500 1 DA A 12 C6 DA A 12 N6 0.096 REMARK 500 1 DC A 13 C4 DC A 13 N4 0.095 REMARK 500 1 DG B 14 C2 DG B 14 N2 0.076 REMARK 500 1 DT B 15 C5 DT B 15 C7 0.037 REMARK 500 1 DG B 16 C2 DG B 16 N2 0.085 REMARK 500 1 DC B 17 C4 DC B 17 N4 0.096 REMARK 500 1 DT B 19 C5 DT B 19 C7 0.047 REMARK 500 1 DG B 20 C2 DG B 20 N2 0.085 REMARK 500 1 DT B 21 C5 DT B 21 C7 0.038 REMARK 500 1 DT B 22 C5 DT B 22 C7 0.039 REMARK 500 1 DG B 24 C2 DG B 24 N2 0.086 REMARK 500 1 DT B 25 C5 DT B 25 C7 0.040 REMARK 500 1 DG B 26 C2 DG B 26 N2 0.087 REMARK 500 2 DC A 1 C4 DC A 1 N4 0.095 REMARK 500 2 DA A 2 C6 DA A 2 N6 0.090 REMARK 500 2 DC A 3 C4 DC A 3 N4 0.091 REMARK 500 2 DA A 4 C6 DA A 4 N6 0.096 REMARK 500 2 DA A 5 C6 DA A 5 N6 0.096 REMARK 500 2 DA A 6 C6 DA A 6 N6 0.092 REMARK 500 2 DC A 7 C4 DC A 7 N4 0.095 REMARK 500 2 DA A 8 C6 DA A 8 N6 0.094 REMARK 500 2 DG A 10 C2 DG A 10 N2 0.082 REMARK 500 2 DC A 11 C4 DC A 11 N4 0.095 REMARK 500 2 DA A 12 C6 DA A 12 N6 0.094 REMARK 500 2 DC A 13 C4 DC A 13 N4 0.094 REMARK 500 2 DG B 14 C2 DG B 14 N2 0.078 REMARK 500 2 DT B 15 C5 DT B 15 C7 0.037 REMARK 500 2 DG B 16 C2 DG B 16 N2 0.086 REMARK 500 2 DC B 17 C4 DC B 17 N4 0.095 REMARK 500 2 DT B 19 C5 DT B 19 C7 0.042 REMARK 500 2 DG B 20 C2 DG B 20 N2 0.082 REMARK 500 2 DT B 22 C5 DT B 22 C7 0.038 REMARK 500 2 DG B 24 C2 DG B 24 N2 0.084 REMARK 500 2 DT B 25 C5 DT B 25 C7 0.038 REMARK 500 2 DG B 26 C2 DG B 26 N2 0.090 REMARK 500 3 DC A 1 C4 DC A 1 N4 0.099 REMARK 500 3 DA A 2 C6 DA A 2 N6 0.084 REMARK 500 3 DC A 3 C4 DC A 3 N4 0.093 REMARK 500 3 DA A 4 C6 DA A 4 N6 0.096 REMARK 500 3 DA A 5 C6 DA A 5 N6 0.095 REMARK 500 REMARK 500 THIS ENTRY HAS 129 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 DA A 2 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC A 3 N1 - C1' - C2' ANGL. DEV. = 8.6 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 8.5 DEGREES REMARK 500 1 DA A 4 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC A 7 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA A 12 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG B 14 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG B 14 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DT B 15 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG B 16 O4' - C1' - C2' ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DG B 16 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DC B 17 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DC B 17 O4' - C1' - N1 ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DT B 19 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG B 20 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG B 20 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DT B 23 C4 - C5 - C7 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT B 23 C6 - C5 - C7 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DG B 24 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG B 24 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG B 24 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DT B 25 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG B 26 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG B 26 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DC A 1 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DA A 2 C5' - C4' - O4' ANGL. DEV. = 7.0 DEGREES REMARK 500 2 DA A 2 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 2 DA A 2 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 8.8 DEGREES REMARK 500 2 DA A 4 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DA A 5 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DA A 6 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DG B 14 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DG B 14 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DG B 16 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DG B 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 DC B 17 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 2 DC B 17 O4' - C1' - N1 ANGL. DEV. = 8.0 DEGREES REMARK 500 2 DT B 19 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 2 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DG B 20 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG B 20 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 167 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FZS RELATED DB: PDB REMARK 900 1FZS CONTAINS A REPLICATION INTERMEDIATE WITH A 3'-TERMINAL REMARK 900 PYRENE RESIDUE PAIRED AT AN ABASIC SITE DBREF 1FZL A 1 13 PDB 1FZL 1FZL 1 13 DBREF 1FZL B 14 26 PDB 1FZL 1FZL 14 26 SEQRES 1 A 13 DC DA DC DA DA DA DC DA PYP DG DC DA DC SEQRES 1 B 13 DG DT DG DC 3DR DT DG DT DT DT DG DT DG HET PYP A 9 43 HET 3DR B 18 19 HETNAM PYP 2'-DEOXYRIBOFURANOSYLPYRENE-5'-MONOPHOSPHATE HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 1 PYP C21 H19 O6 P FORMUL 2 3DR C5 H11 O6 P LINK O3' DA A 8 P PYP A 9 1555 1555 1.62 LINK O3' PYP A 9 P DG A 10 1555 1555 1.62 LINK O3' DC B 17 P 3DR B 18 1555 1555 1.62 LINK O3' 3DR B 18 P DT B 19 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 197 0 2 0 0 0 0 6 0 0 0 2 END