HEADER DNA 01-APR-98 1A83 TITLE INTRAMOLECULAR I-MOTIF, NMR, 6 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-(MCY)CTTTCCTTTACCTTTCC-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE INTRAMOLECULAR FOLDING OF THIS I-MOTIF MAY RELATED COMPND 6 TO THE CYTOSINE-RICH STRANDS OF TELOMERES AND HUMAN CENTROMERE. THE COMPND 7 FIRST CYTOSINE IS C5-METHYLATED AND IS NAMED MCY IN THIS ENTRY. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DEOXYRIBONUCLEIC ACID, DNA, I-MOTIF, SOLUTION STRUCTURE, TELOMERE, KEYWDS 2 CENTROMERE EXPDTA SOLUTION NMR NUMMDL 6 AUTHOR X.HAN,J.L.LEROY,M.GUERON REVDAT 4 22-MAY-24 1A83 1 REMARK REVDAT 3 16-FEB-22 1A83 1 REMARK LINK REVDAT 2 24-FEB-09 1A83 1 VERSN REVDAT 1 17-JUN-98 1A83 0 JRNL AUTH X.HAN,J.L.LEROY,M.GUERON JRNL TITL AN INTRAMOLECULAR I-MOTIF: THE SOLUTION STRUCTURE AND JRNL TITL 2 BASE-PAIR OPENING KINETICS OF D(5MCCT3CCT3ACCT3CC). JRNL REF J.MOL.BIOL. V. 278 949 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9600855 JRNL DOI 10.1006/JMBI.1998.1740 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.0 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A83 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_1000170510. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 270; 270 REMARK 210 PH : 4.8; 7.0 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : NULL; NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; HETERO-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 6 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST ENERGY OF NOE VIOLATION 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: 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 REMARK 500 REMARK: NULL 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 2 DT A 10 C5 DT A 10 C7 0.036 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 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA A 11 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA A 11 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 12 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DC A 13 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC A 13 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC A 13 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 14 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 15 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT A 16 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC A 17 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC A 18 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DA A 11 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DA A 11 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DC A 12 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DC A 13 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DC A 13 C2 - N3 - C4 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DC A 13 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DT A 14 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DT A 15 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT A 16 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC A 17 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DC A 18 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DC A 2 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 131 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 DC A 2 0.08 SIDE CHAIN REMARK 500 3 DC A 2 0.07 SIDE CHAIN REMARK 500 5 DC A 2 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1A83 A 1 18 PDB 1A83 1A83 1 18 SEQRES 1 A 18 MCY DC DT DT DT DC DC DT DT DT DA DC DC SEQRES 2 A 18 DT DT DT DC DC MODRES 1A83 MCY A 1 DC 5-METHYL-2'-DEOXYCYTIDINE HET MCY A 1 31 HETNAM MCY 5-METHYL-2'-DEOXYCYTIDINE FORMUL 1 MCY C10 H15 N3 O4 LINK O3' MCY A 1 P DC A 2 1555 1555 1.61 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 HETATM 1 N1 MCY A 1 -2.238 1.006 -2.349 1.00 0.00 N HETATM 2 C2 MCY A 1 -2.473 0.837 -1.002 1.00 0.00 C HETATM 3 N3 MCY A 1 -2.265 -0.404 -0.492 1.00 0.00 N HETATM 4 C4 MCY A 1 -1.842 -1.424 -1.281 1.00 0.00 C HETATM 5 C5 MCY A 1 -1.620 -1.222 -2.584 1.00 0.00 C HETATM 6 C6 MCY A 1 -1.825 -0.023 -3.105 1.00 0.00 C HETATM 7 O2 MCY A 1 -2.858 1.771 -0.303 1.00 0.00 O HETATM 8 N4 MCY A 1 -1.671 -2.640 -0.776 1.00 0.00 N HETATM 9 C1' MCY A 1 -2.406 2.337 -2.955 1.00 0.00 C HETATM 10 C2' MCY A 1 -1.087 2.813 -3.541 1.00 0.00 C HETATM 11 C3' MCY A 1 -1.305 3.034 -5.015 1.00 0.00 C HETATM 12 C4' MCY A 1 -2.768 2.710 -5.275 1.00 0.00 C HETATM 13 O4' MCY A 1 -3.365 2.287 -4.031 1.00 0.00 O HETATM 14 O3' MCY A 1 -1.003 4.388 -5.375 1.00 0.00 O HETATM 15 C5' MCY A 1 -2.908 1.618 -6.334 1.00 0.00 C HETATM 16 O5' MCY A 1 -2.698 2.130 -7.653 1.00 0.00 O HETATM 17 C5A MCY A 1 -1.101 -2.356 -3.467 1.00 0.00 C HETATM 18 H6 MCY A 1 -1.700 0.123 -4.153 1.00 0.00 H HETATM 19 HN41 MCY A 1 -1.374 -3.398 -1.371 1.00 0.00 H HETATM 20 HN42 MCY A 1 -1.858 -2.808 0.185 1.00 0.00 H HETATM 21 H1' MCY A 1 -2.745 3.040 -2.199 1.00 0.00 H HETATM 22 H2' MCY A 1 -0.317 2.057 -3.388 1.00 0.00 H HETATM 23 H2'' MCY A 1 -0.789 3.739 -3.070 1.00 0.00 H HETATM 24 H3' MCY A 1 -0.673 2.346 -5.582 1.00 0.00 H HETATM 25 H4' MCY A 1 -3.275 3.610 -5.623 1.00 0.00 H HETATM 26 H5' MCY A 1 -2.177 0.834 -6.137 1.00 0.00 H HETATM 27 H5'' MCY A 1 -3.909 1.192 -6.275 1.00 0.00 H HETATM 28 HO5' MCY A 1 -1.891 2.649 -7.631 1.00 0.00 H HETATM 29 H5A1 MCY A 1 -1.594 -2.313 -4.438 1.00 0.00 H HETATM 30 H5A2 MCY A 1 -1.311 -3.316 -2.997 1.00 0.00 H HETATM 31 H5A3 MCY A 1 -0.025 -2.247 -3.604 1.00 0.00 H