HEADER DNA 22-NOV-02 1N96 TITLE DIMERIC SOLUTION STRUCTURE OF THE CYCLIC OCTAMER TITLE 2 CD(CGCTCATT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIC OLIGONUCLEOTIDE D(CGCTCATT); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS QUADRUPLEX, FOUR-STRANDED DNA, UNUSUAL DNA, BI-LOOP EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR N.ESCAJA,J.L.GELPI,M.OROZCO,M.RICO,E.PEDROSO,C.GONZALEZ REVDAT 2 24-FEB-09 1N96 1 VERSN REVDAT 1 13-MAY-03 1N96 0 JRNL AUTH N.ESCAJA,J.L.GELPI,M.OROZCO,M.RICO,E.PEDROSO, JRNL AUTH 2 C.GONZALEZ JRNL TITL FOUR-STRANDED DNA STRUCTURE STABILIZED BY A NOVEL JRNL TITL 2 G:C:A:T TETRAD. JRNL REF J.AM.CHEM.SOC. V. 125 5654 2003 JRNL REFN ISSN 0002-7863 JRNL PMID 12733903 JRNL DOI 10.1021/JA0344157 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.ESCAJA,E.PEDROSO,M.RICO,C.GONZALEZ REMARK 1 TITL DIMERIC SOLUTION STRUCTURE OF TWO CYCLIC OCTAMERS: REMARK 1 TITL 2 FOUR STRANDED DNA STRUCTURES STABILIZED BY A:T:A:T REMARK 1 TITL 3 AND C:G:C:G TETRADS REMARK 1 REF J.AM.CHEM.SOC. V. 122 12732 2000 REMARK 1 REFN ISSN 0002-7863 REMARK 1 DOI 10.1021/JA002778Q REMARK 1 REFERENCE 2 REMARK 1 AUTH C.GONZALEZ,N.ESCAJA,M.RICO,E.PEDROSO REMARK 1 TITL NMR STRUCTURE OF TWO CYCLIC OLIGONUCLEOTIDES. A REMARK 1 TITL 2 MONOMER DIMER EQUILIBRIUM BETWEEN DUMBELLL AND REMARK 1 TITL 3 QUADRUPLEX STRUCTURES REMARK 1 REF J.AM.CHEM.SOC. V. 120 2176 1998 REMARK 1 REFN ISSN 0002-7863 REMARK 1 DOI 10.1021/JA973691G REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 5.1 REMARK 3 AUTHORS : D. PEARLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SEE REFERENCES REMARK 4 REMARK 4 1N96 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-02. REMARK 100 THE RCSB ID CODE IS RCSB017674. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 5MM D, PHOSPHATE REMARK 210 BUFFER, 100 MM NACL; 5MM D< REMARK 210 PCGCTCATT>, PHOSPHATE BUFFER, REMARK 210 100 MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MARDIGRAS, DYANA 1.5 REMARK 210 METHOD USED : RELAXATION MATRIX REMARK 210 CALCULATIONS RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 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 C5' - C4' - O4' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DT A 7 C4 - C5 - C7 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG B 2 O4' - C1' - N9 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT B 4 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DT B 4 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT B 7 C4 - C5 - C7 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT B 7 C6 - C5 - C7 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DT B 8 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = -5.9 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DT A 7 C4 - C5 - C7 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DT A 7 C6 - C5 - C7 ANGL. DEV. = -5.5 DEGREES REMARK 500 2 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG B 2 O4' - C1' - N9 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 DT B 4 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 2 DT B 4 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DC B 5 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DA B 6 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT B 7 C4 - C5 - C7 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DT B 7 C6 - C5 - C7 ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DT B 8 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 3 DC A 5 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 3 DT A 7 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES REMARK 500 3 DT A 8 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 DG B 2 C5' - C4' - O4' ANGL. DEV. = 7.2 DEGREES REMARK 500 3 DG B 2 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 3 DT B 4 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 3 DT B 4 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 3 DC B 5 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DA B 6 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DT B 7 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 3 DT B 8 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 DG A 2 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 4 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 4 DC A 5 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 4 DA A 6 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 4 DA A 6 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES REMARK 500 4 DT A 7 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES REMARK 500 4 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 148 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 1 DC A 1 0.08 SIDE_CHAIN REMARK 500 1 DT A 4 0.12 SIDE_CHAIN REMARK 500 1 DC A 5 0.12 SIDE_CHAIN REMARK 500 1 DA A 6 0.11 SIDE_CHAIN REMARK 500 1 DT B 4 0.11 SIDE_CHAIN REMARK 500 1 DA B 6 0.08 SIDE_CHAIN REMARK 500 1 DT B 8 0.08 SIDE_CHAIN REMARK 500 2 DT A 8 0.06 SIDE_CHAIN REMARK 500 2 DT B 8 0.09 SIDE_CHAIN REMARK 500 3 DA A 6 0.07 SIDE_CHAIN REMARK 500 3 DT A 8 0.08 SIDE_CHAIN REMARK 500 3 DT B 4 0.09 SIDE_CHAIN REMARK 500 3 DA B 6 0.06 SIDE_CHAIN REMARK 500 4 DT A 4 0.07 SIDE_CHAIN REMARK 500 4 DC A 5 0.10 SIDE_CHAIN REMARK 500 4 DA A 6 0.09 SIDE_CHAIN REMARK 500 4 DC B 5 0.10 SIDE_CHAIN REMARK 500 5 DT B 4 0.07 SIDE_CHAIN REMARK 500 6 DC A 5 0.07 SIDE_CHAIN REMARK 500 6 DC B 5 0.12 SIDE_CHAIN REMARK 500 6 DT B 8 0.06 SIDE_CHAIN REMARK 500 7 DC A 5 0.08 SIDE_CHAIN REMARK 500 7 DT A 8 0.07 SIDE_CHAIN REMARK 500 7 DT B 8 0.09 SIDE_CHAIN REMARK 500 8 DA A 6 0.07 SIDE_CHAIN REMARK 500 8 DT A 8 0.08 SIDE_CHAIN REMARK 500 8 DT B 7 0.08 SIDE_CHAIN REMARK 500 9 DT A 8 0.06 SIDE_CHAIN REMARK 500 10 DT A 4 0.09 SIDE_CHAIN REMARK 500 10 DT A 8 0.08 SIDE_CHAIN REMARK 500 10 DT B 4 0.09 SIDE_CHAIN REMARK 500 10 DT B 8 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EU2 RELATED DB: PDB REMARK 900 RELATED ID: 1EU6 RELATED DB: PDB DBREF 1N96 A 1 8 PDB 1N96 1N96 1 8 DBREF 1N96 B 1 8 PDB 1N96 1N96 1 8 SEQRES 1 A 8 DC DG DC DT DC DA DT DT SEQRES 1 B 8 DC DG DC DT DC DA DT DT LINK O3' DT A 8 P DC A 1 1555 1555 1.61 LINK O3' DT B 8 P DC B 1 1555 1555 1.60 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 ENDMDL ENDMDL ENDMDL ENDMDL MASTER 187 0 0 0 0 0 0 6 0 0 0 2 END