1Q2T - Header Asymmetric Unit

HEADER DNA 26-JUL-03 1Q2T

TITLE SOLUTION STRUCTURE OF D(5MCCTCTCC)4

COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*(MCY)P*CP*TP*CP*TP*CP*C)-3'; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES

KEYWDS DNA SOLUTION STRUCTURE; I-MOTIF; PROTONATED CYTIDINE; KEYWDS 2 HEMIPROTONATED BASE-PAIRS

EXPDTA SOLUTION NMR

AUTHOR J.-L.LEROY

REVDAT 2 24-FEB-09 1Q2T 1 VERSN REVDAT 1 23-SEP-03 1Q2T 0

JRNL AUTH J.-L.LEROY JRNL TITL T.T PAIR INTERCALATION AND DUPLEX INTER-CONVERSION JRNL TITL 2 WITHIN I-MOTIF TETRAMERS JRNL REF J.MOL.BIOL. V. 333 125 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 14516748 JRNL DOI 10.1016/S0022-2836(03)00945-8

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.NONIN,J.-L.LEROY REMARK 1 TITL STRUCTURE AND CONVERSION KINETICS OF A BI-STABLE REMARK 1 TITL 2 DNA I-MOTIF: BROKEN SYMMETRY IN THE [D(5MCCTCC)]4 REMARK 1 TITL 3 TETRAMER. REMARK 1 REF J.MOL.BIOL. V. 261 399 1996 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1996.0472

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A TOTAL OF REMARK 3 172 RESTRAINTS. 30 BASE-PAIRING RESTRAINTS FROM HYDROGEN REMARK 3 BONDS, 78 NOE-DISTANCE RESTRAINTS AND 36 REPULSIVE RESTRAINTS REMARK 3 REFLECTING THE ABSENCE OF NOE

REMARK 4 REMARK 4 1Q2T COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-03. REMARK 100 THE RCSB ID CODE IS RCSB019844.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273 REMARK 210 PH : 4.4 REMARK 210 IONIC STRENGTH : NO ADDED COUNTER-IONS REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 10MM DNA STRAND REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.851 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE REMARK 210 WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM 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 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC A 2 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC A 4 C2 - N3 - C4 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC A 4 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC A 6 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC A 7 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC A 7 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC B 2 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC B 2 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC B 2 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT B 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 4 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC B 4 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT B 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 6 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC B 6 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 7 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC B 7 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC C 2 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT C 3 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC C 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT C 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC C 6 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC C 7 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC D 2 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT D 3 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC D 4 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT D 5 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC D 6 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC D 7 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES 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 DC B 2 0.07 SIDE_CHAIN REMARK 500 DC D 2 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RME RELATED DB: PDB REMARK 900 I-MOTIF TETRAMER OF 5MCCTCC

DBREF 1Q2T A 1 7 PDB 1Q2T 1Q2T 1 7 DBREF 1Q2T B 1 7 PDB 1Q2T 1Q2T 1 7 DBREF 1Q2T C 1 7 PDB 1Q2T 1Q2T 1 7 DBREF 1Q2T D 1 7 PDB 1Q2T 1Q2T 1 7

SEQRES 1 A 7 MCY DC DT DC DT DC DC SEQRES 1 B 7 MCY DC DT DC DT DC DC SEQRES 1 C 7 MCY DC DT DC DT DC DC SEQRES 1 D 7 MCY DC DT DC DT DC DC

MODRES 1Q2T MCY A 1 DC 5-METHYL-2'-DEOXYCYTIDINE MODRES 1Q2T MCY B 1 DC 5-METHYL-2'-DEOXYCYTIDINE MODRES 1Q2T MCY C 1 DC 5-METHYL-2'-DEOXYCYTIDINE MODRES 1Q2T MCY D 1 DC 5-METHYL-2'-DEOXYCYTIDINE

HET MCY A 1 31 HET MCY B 1 31 HET MCY C 1 31 HET MCY D 1 31

HETNAM MCY 5-METHYL-2'-DEOXYCYTIDINE

FORMUL 1 MCY 4(C10 H15 N3 O4)

LINK O3' MCY A 1 P DC A 2 1555 1555 1.61 LINK O3' MCY B 1 P DC B 2 1555 1555 1.61 LINK O3' MCY C 1 P DC C 2 1555 1555 1.61 LINK O3' MCY D 1 P DC D 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