HEADER DNA 08-APR-03 1OZ8 TITLE INTRAMOLECULAR HIGHER-ORDER PACKING OF PARALLEL QUADRUPLEXES TITLE 2 COMPRISING A G:G:G:G TETRAD AND A G(:A):G(:A):G(:A):G HEPTAD OF GGA TITLE 3 TRIPLET REPEAT DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*AP COMPND 3 *GP*GP*AP*GP*GP*A)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS INTRAMOLECULAR PACKING OF PARALLEL QUADRUPLEXES, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.MATSUGAMI,T.OKUIZUMI,S.UESUGI,M.KATAHIRA REVDAT 4 29-MAY-24 1OZ8 1 REMARK REVDAT 3 23-FEB-22 1OZ8 1 REMARK REVDAT 2 24-FEB-09 1OZ8 1 VERSN REVDAT 1 08-APR-04 1OZ8 0 JRNL AUTH A.MATSUGAMI,T.OKUIZUMI,S.UESUGI,M.KATAHIRA JRNL TITL INTRAMOLECULAR HIGHER ORDER PACKING OF PARALLEL QUADRUPLEXES JRNL TITL 2 COMPRISING A G:G:G:G TETRAD AND A G(:A):G(:A):G(:A):G HEPTAD JRNL TITL 3 OF GGA TRIPLET REPEAT DNA JRNL REF J.BIOL.CHEM. V. 278 28147 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12748183 JRNL DOI 10.1074/JBC.M303694200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.MATSUGAMI,K.OUHASHI,M.KANAGAWA,H.LIU,S.KANAGAWA,S.UESUGI, REMARK 1 AUTH 2 M.KATAHIRA REMARK 1 TITL AN INTRAMOLECULAR QUADRUPLEX OF (GGA)(4) TRIPLET REPEAT DNA REMARK 1 TITL 2 WITH A G:G:G:G TETRAD AND A G(:A):G(:A):G(:A):G HEPTAD, AND REMARK 1 TITL 3 ITS DIMERIC INTERACTION REMARK 1 REF J.MOL.BIOL. V. 313 255 2001 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 11800555 REMARK 1 DOI 10.1006/JMBI.2001.5047 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.LIU,A.MATSUGAMI,M.KATAHIRA,S.UESUGI REMARK 1 TITL A DIMERIC RNA QUADRUPLEX ARCHITECTURE COMPRISED OF TWO REMARK 1 TITL 2 G:G(:A):G:G(:A) HEXADS, G:G:G:G TETRADS AND UUUU LOOPS REMARK 1 REF J.MOL.BIOL. V. 322 955 2002 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 12367521 REMARK 1 DOI 10.1016/S0022-2836(02)00876-8 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851, X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OZ8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000018828. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 275; 298 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM DNA; 10MM SODIUM PHOSPHATE REMARK 210 BUFFER; 30MM KCL; 1MM DNA; 10MM REMARK 210 SODIUM PHOSPHATE BUFFER; 30MM KCL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 H4' DG A 11 O4' DA A 12 1.44 REMARK 500 H61 DA A 9 O4' DG A 16 1.50 REMARK 500 O4' DG A 10 H61 DA A 15 1.54 REMARK 500 H21 DG A 19 N7 DG A 22 1.56 REMARK 500 H21 DG A 17 N7 DG A 20 1.57 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. = 3.4 DEGREES REMARK 500 1 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 1 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DA A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DA A 6 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 6 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG A 7 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DA A 9 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 10 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DA A 12 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 13 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 13 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 14 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DA A 15 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA A 15 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 15 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG A 17 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DA A 18 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA A 18 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 19 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DG A 19 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 20 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 20 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DA A 21 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 22 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1126 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1OZ8 A 1 24 PDB 1OZ8 1OZ8 1 24 SEQRES 1 A 24 DG DG DA DG DG DA DG DG DA DG DG DA DG SEQRES 2 A 24 DG DA DG DG DA DG DG DA DG DG DA 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