HEADER DNA 25-JUN-09 2KKK TITLE AN I-MOTIF STRUCTURE WITH INTERCALATED T T PAIRS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*(MCY)P*CP*TP*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 EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.LEROY,M.CANALIA REVDAT 1 04-AUG-09 2KKK 0 JRNL AUTH J.LEROY,M.CANALIA JRNL TITL [5MCCTCTCTCC]4: AN I-MOTIF TETRAMER WITH JRNL TITL 2 INTERCALATED T T PAIRS. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 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: NULL REMARK 4 REMARK 4 2KKK COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-JUL-09. REMARK 100 THE RCSB ID CODE IS RCSB101235. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 5 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2-5 MM DNA, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H 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 : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS COMPUTED USING DISTANCE RESTRAINTS REMARK 210 DERIVED FROM NOE IN H2O AND IN D2O 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 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 7 DT A 7 C5 DT A 7 C7 0.037 REMARK 500 7 DT B 7 C5 DT B 7 C7 0.038 REMARK 500 7 DT D 7 C5 DT D 7 C7 0.037 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. = 2.5 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC B 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT B 3 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC B 4 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT B 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC B 6 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT B 7 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC B 8 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC B 9 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC C 2 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT C 3 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC C 4 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT C 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC C 6 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT C 7 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC C 8 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC C 9 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC D 2 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT D 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC D 4 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT D 5 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC D 6 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT D 7 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC D 8 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC D 9 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DC A 8 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC B 2 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DT B 3 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DC B 4 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DT B 5 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC B 6 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT B 7 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DC B 8 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC B 9 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC C 2 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DT C 3 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 309 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 4 DT A 5 0.07 SIDE_CHAIN REMARK 500 4 DT B 5 0.07 SIDE_CHAIN REMARK 500 4 DT C 5 0.07 SIDE_CHAIN REMARK 500 4 DT D 5 0.07 SIDE_CHAIN REMARK 500 7 DC A 4 0.06 SIDE_CHAIN REMARK 500 7 DC C 4 0.06 SIDE_CHAIN REMARK 500 7 DC D 4 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Q2T RELATED DB: PDB DBREF 2KKK A 1 9 PDB 2KKK 2KKK 1 9 DBREF 2KKK B 1 9 PDB 2KKK 2KKK 1 9 DBREF 2KKK C 1 9 PDB 2KKK 2KKK 1 9 DBREF 2KKK D 1 9 PDB 2KKK 2KKK 1 9 SEQRES 1 A 9 MCY DC DT DC DT DC DT DC DC SEQRES 1 B 9 MCY DC DT DC DT DC DT DC DC SEQRES 1 C 9 MCY DC DT DC DT DC DT DC DC SEQRES 1 D 9 MCY DC DT DC DT DC DT DC DC MODRES 2KKK MCY A 1 DC 5-METHYL-2'-DEOXYCYTIDINE MODRES 2KKK MCY B 1 DC 5-METHYL-2'-DEOXYCYTIDINE MODRES 2KKK MCY C 1 DC 5-METHYL-2'-DEOXYCYTIDINE MODRES 2KKK 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 163 0 4 0 0 0 0 6 0 0 0 4 END