HEADER PEPTIDE NUCLEIC ACID/DNA 28-MAR-96 1PDT TITLE PD235, PNA-DNA DUPLEX, NMR, 8 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*AP*CP*AP*TP*AP*GP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PEPTIDE NUCLEIC ACID (COOH-P(*G*C*T*A*T*G*T*C)-NH2); COMPND 7 CHAIN: B; COMPND 8 SYNONYM: PNA; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: PNA-DNA DUPLEX SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS COMPLEX (PEPTIDE NUCLEIC ACID-DNA), NUCLEIC ACID COMPLEX, DUPLEX, KEYWDS 2 HYBRID, PEPTIDE NUCLEIC ACID-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR M.ERIKSSON,P.E.NIELSEN REVDAT 4 15-NOV-23 1PDT 1 REMARK LINK ATOM REVDAT 3 13-JUL-11 1PDT 1 VERSN REVDAT 2 24-FEB-09 1PDT 1 VERSN REVDAT 1 14-OCT-96 1PDT 0 JRNL AUTH M.ERIKSSON,P.E.NIELSEN JRNL TITL SOLUTION STRUCTURE OF A PEPTIDE NUCLEIC ACID-DNA DUPLEX. JRNL REF NAT.STRUCT.BIOL. V. 3 410 1996 JRNL REFN ISSN 1072-8368 JRNL PMID 8612069 JRNL DOI 10.1038/NSB0596-410 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.LEIJON,A.GRASLUND,P.E.NIELSEN,O.BUCHARDT,B.NORDEN, REMARK 1 AUTH 2 S.M.KRISTENSEN,M.ERIKSSON REMARK 1 TITL STRUCTURAL CHARACTERIZATION OF PNA-DNA DUPLEXES BY NMR. REMARK 1 TITL 2 EVIDENCE FOR DNA IN A B-LIKE CONFORMATION REMARK 1 REF BIOCHEMISTRY V. 33 9820 1994 REMARK 1 REFN ISSN 0006-2960 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 1PDT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175619. 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 : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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: 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 O4' DC A 3 HN1 NH2 B 17 1.54 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 1 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA A 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DA A 2 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DA A 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 3 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DG A 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 DA A 2 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 4 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 4 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 4 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 4 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 5 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 DA A 2 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 5 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 5 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 5 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 5 DA A 6 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 5 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 DA A 2 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 6 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 6 DA A 4 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 72 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 DG A 7 0.05 SIDE CHAIN REMARK 500 4 DG A 7 0.05 SIDE CHAIN REMARK 500 6 DG A 7 0.05 SIDE CHAIN REMARK 500 7 DA A 4 0.05 SIDE CHAIN REMARK 500 8 DG A 7 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 B 17 DBREF 1PDT A 1 8 PDB 1PDT 1PDT 1 8 DBREF 1PDT B 9 17 PDB 1PDT 1PDT 9 17 SEQRES 1 A 8 DG DA DC DA DT DA DG DC SEQRES 1 B 9 GPN CPN TPN APN TPN GPN TPN CPN NH2 MODRES 1PDT GPN B 9 DG MODRES 1PDT CPN B 10 DC MODRES 1PDT TPN B 11 DT MODRES 1PDT APN B 12 DA MODRES 1PDT TPN B 13 DT MODRES 1PDT GPN B 14 DG MODRES 1PDT TPN B 15 DT MODRES 1PDT CPN B 16 DC HET GPN B 9 35 HET CPN B 10 31 HET TPN B 11 33 HET APN B 12 33 HET TPN B 13 33 HET GPN B 14 34 HET TPN B 15 33 HET CPN B 16 31 HET NH2 B 17 3 HETNAM GPN 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE HETNAM CPN 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE HETNAM TPN 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE HETNAM APN 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE HETNAM NH2 AMINO GROUP FORMUL 2 GPN 2(C11 H16 N7 O4 1+) FORMUL 2 CPN 2(C10 H16 N5 O4 1+) FORMUL 2 TPN 3(C11 H17 N4 O5 1+) FORMUL 2 APN C11 H16 N7 O3 1+ FORMUL 2 NH2 H2 N LINK C GPN B 9 N CPN B 10 1555 1555 1.31 LINK C CPN B 10 N TPN B 11 1555 1555 1.31 LINK C TPN B 11 N APN B 12 1555 1555 1.31 LINK C APN B 12 N TPN B 13 1555 1555 1.31 LINK C TPN B 13 N GPN B 14 1555 1555 1.31 LINK C GPN B 14 N TPN B 15 1555 1555 1.31 LINK C TPN B 15 N CPN B 16 1555 1555 1.31 LINK C CPN B 16 N NH2 B 17 1555 1555 1.30 LINK O CPN B 16 N NH2 B 17 1555 1555 1.09 SITE 1 AC1 2 DC A 3 CPN B 16 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