HEADER DEOXYRIBONUCLEIC ACID 24-APR-92 1D71 TITLE A THREE-DIMENSIONAL MODEL FOR NODULE DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (47-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (47-MER); 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 DNA EXPDTA THEORETICAL MODEL AUTHOR D.SPROUS,S.C.HARVEY REVDAT 2 15-OCT-94 1D71 1 COMPND REVDAT 1 15-JUL-93 1D71 0 JRNL AUTH D.SPROUS,S.C.HARVEY JRNL TITL A THREE-DIMENSIONAL MODEL FOR NODULE DNA. JRNL REF J.BIOL.CHEM. V. 267 5502 1992 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.G.PANYUTIN,R.D.WELLS REMARK 1 TITL NODULE DNA IN THE (GA)37(CT)37 INSERT IN REMARK 1 TITL 2 SUPERHELICAL PLASMIDS REMARK 1 REF J.BIOL.CHEM. V. 267 5495 1992 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.A.BEAL,P.B.DERVAN REMARK 1 TITL SECOND STRUCTURAL MOTIF FOR RECOGNITION OF DNA BY REMARK 1 TITL 2 OLIGONUCLEOTIDE-DIRECTED TRIPLE-HELIX FORMATION REMARK 1 REF SCIENCE V. 251 1360 1991 REMARK 1 REFN ASTM SCIEAS US ISSN 0036-8075 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.ARNOTT,E.SELSING REMARK 1 TITL STRUCTURES FOR THE POLYNUCLEOTIDE COMPLEXES REMARK 1 TITL 2 POLY(DA)POLY(DT) AND POLY(DT)POLY(DA)POLY(DT) REMARK 1 REF J.MOL.BIOL. V. 88 509 1974 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 4 REMARK 1 AUTH R.LAVERY REMARK 1 TITL DNA FLEXIBILITY UNDER CONTROL: THE JUMNA ALGORITHM REMARK 1 TITL 2 AND ITS APPLICATION TO BZ JUNCTIONS REMARK 1 EDIT R.D.WELLS, S.C.HARVEY REMARK 1 REF UNUSUAL DNA STRUCTURES 189 1987 REMARK 1 PUBL SPRINGER-VERLAG, NEW YORK, NEW YORK REMARK 1 REFN ISBN 0-387-96631-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1D71 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 IN THE B CHAIN THE RESIDUES ARE NUMBERED STARTING AT THE 3' REMARK 5 TERMINUS. THE RESIDUES ARE STORED IN STANDARD PDB FORM REMARK 5 STARTING AT THE 5' TERMINUS. THUS THE RESIDUE NUMBERING IN REMARK 5 THE B CHAIN GOES FROM 94 TO 48. REMARK 6 REMARK 6 THIS STRUCTURE IS A BITRIPLEX SYSTEM WITH STRAND EXCHANGE REMARK 6 THE FIRST TRIPLEX IS BASED UPON THE Y:R.Y MODEL OF BEAL REMARK 6 AND DERVAN (REF 3) WHERE Y=PYRIMIDINE, R=PURINE, COLON (:) REMARK 6 INDICATES WATSON-CRICK BASEPAIRING AND PERIOD (.) INDICATES REMARK 6 ASSOCIATION OF THIRD STRAND BOUND IN MAJOR GROOVE OF REMARK 6 WATSON-CRICK DUPLEX. REMARK 6 REMARK 6 THE SECOND TRIPLEX IS BASED UPON FIBER DIFFRACTION DATA OF REMARK 6 ARNOTT AND SELSING (REF 4) FOR Y:R.Y DNA TRIPLEX. REMARK 6 THESE WERE ASSEMBLED AND REFINED BY A MODIFIED VERSION OF REMARK 6 JUMNA IV (REF 6) WHERE THE MAXIMUM NUMBER OF NUCLEOTIDES REMARK 6 WAS INCREASED BY ARUN MALHOTRA REMARK 6 REMARK 6 STRAND 1 (RESIDUES 1-47): 5'-3' REMARK 6 REMARK 6 GAGAG AGAGA GAGAG AGAGA GAGAG AGAGA GAGAG AGAGA GAGAG AG REMARK 6 STRAND 2 (RESIDUES 48-94): 3'-5' REMARK 6 REMARK 6 CTCTC TCTCT CTCTC TCTCT CTCTC TCTCT CTCTC TCTCT CTCTC TC REMARK 6 REMARK 6 DUPLEX REGIONS = 2 (WATSON-CRICK) REMARK 6 1 48 5 52 REMARK 6 43 90 47 94 REMARK 6 REMARK 6 TRIPLEX REGIONS = 2 (WATSON-CRICK, WITH THIRD STRAND IN REMARK 6 MAJOR GROOVE OF DUPLEX) REMARK 6 6 53 28 14 61 20 REMARK 6 34 75 81 42 67 89 REMARK 6 REMARK 6 CONNECTING STRANDS = 4 REMARK 6 15 19 REMARK 6 29 33 REMARK 6 62 66 REMARK 6 76 80 REMARK 7 REMARK 7 CORRECTION. REVISE THEORETICAL MODEL INFORMATION ON COMPND REMARK 7 RECORD. 15-OCT-94. REMARK 103 REMARK 103 THERE ARE NON-WATSON-CRICK HYDROGEN BONDS BETWEEN THE REMARK 103 FOLLOWING ATOMS: REMARK 103 N6 A A 6 AND N1 A A 28 REMARK 103 N7 A A 6 AND N6 A A 28 REMARK 103 N7 G A 7 AND N1 G A 27 REMARK 103 O6 G A 7 AND N2 G A 27 REMARK 103 N6 A A 8 AND N1 A A 26 REMARK 103 N7 A A 8 AND N6 A A 26 REMARK 103 N7 G A 9 AND N1 G A 25 REMARK 103 O6 G A 9 AND N2 G A 25 REMARK 103 N6 A A 10 AND N1 A A 24 REMARK 103 N7 A A 10 AND N6 A A 24 REMARK 103 N7 G A 11 AND N1 G A 23 REMARK 103 O6 G A 11 AND N2 G A 23 REMARK 103 N6 A A 12 AND N1 A A 22 REMARK 103 N7 A A 12 AND N6 A A 22 REMARK 103 N7 G A 13 AND N1 G A 21 REMARK 103 O6 G A 13 AND N2 G A 21 REMARK 103 N6 A A 14 AND N1 A A 20 REMARK 103 N7 A A 14 AND N6 A A 20 REMARK 103 N7 G A 15 AND N1 G A 19 REMARK 103 O6 G A 15 AND N2 G A 19 REMARK 103 N2 G A 19 AND O4 T B 63 REMARK 103 O6 G A 33 AND N4 C B 76 REMARK 103 N6 A A 34 AND O4 T B 75 REMARK 103 N7 A A 34 AND N3 T B 75 REMARK 103 N6 A A 36 AND O4 T B 73 REMARK 103 N7 A A 36 AND N3 T B 73 REMARK 103 O6 G A 37 AND N4 C B 72 REMARK 103 N6 A A 38 AND O4 T B 71 REMARK 103 N7 A A 38 AND N3 T B 71 REMARK 103 O6 G A 39 AND N4 C B 70 REMARK 103 N6 A A 40 AND O4 T B 69 REMARK 103 O6 G A 41 AND N4 C B 68 REMARK 103 N6 A A 42 AND O4 T B 67 REMARK 103 N7 A A 42 AND N3 T B 67 REMARK 103 N3 T B 79 AND O4 T B 77 REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 G A 1 O5* REMARK 470 C B 94 O5* SEQRES 1 A 47 G A G A G A G A G A G A G SEQRES 2 A 47 A G A G A G A G A G A G A SEQRES 3 A 47 G A G A G A G A G A G A G SEQRES 4 A 47 A G A G A G A G SEQRES 1 B 47 C T C T C T C T C T C T C SEQRES 2 B 47 T C T C T C T C T C T C T SEQRES 3 B 47 C T C T C T C T C T C T C SEQRES 4 B 47 T C T C T C T C 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 142 0 0 0 0 0 0 6 0 0 0 8 END