HEADER DNA 02-SEP-05 2AWV TITLE NMR STRUCTURAL ANALYSIS OF THE DIMER OF 5MCCTCATCC COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*(MCY)P*CP*TP*CP*AP*CP*TP*CP*C)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALY SYNTHETIZED USING THE PHOSPHORAMIDITE SOURCE 4 METHOD KEYWDS I-MOTIF, HEMIPROTONATED CC+ PAIRS, DIMER, DNA EXPDTA SOLUTION NMR AUTHOR M.CANALIA,J.-L.LEROY REVDAT 5 29-MAY-24 2AWV 1 REMARK REVDAT 4 09-MAR-22 2AWV 1 REMARK LINK REVDAT 3 24-FEB-09 2AWV 1 VERSN REVDAT 2 01-NOV-05 2AWV 1 JRNL REVDAT 1 20-SEP-05 2AWV 0 JRNL AUTH M.CANALIA,J.-L.LEROY JRNL TITL STRUCTURE, INTERNAL MOTIONS AND ASSOCIATION-DISSOCIATION JRNL TITL 2 KINETICS OF THE I-MOTIF DIMER OF D(5MCCTCACTCC). JRNL REF NUCLEIC ACIDS RES. V. 33 5471 2005 JRNL REFN ISSN 0305-1048 JRNL PMID 16204453 JRNL DOI 10.1093/NAR/GKI843 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 97.2, X-PLOR 3.851 REMARK 3 AUTHORS : HARE D. (FELIX), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON 565 NOE REMARK 3 -DERIVED, DISTANCE CONSTRAINTS, 17 DIHEDRAL ANGLE RESTRAINTS, 20 REMARK 3 DISTANCE RESTRAINTS FROM HYDROGEN BONDS. REMARK 4 REMARK 4 2AWV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034409. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 1 NA / PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : STRAND CONCENTRATION: 0.1 TO REMARK 210 10MM REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; E-COSY; 1H-31P COSY 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, MOLMOL 2.4 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 WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR AND HETERONUCLEAR TECHNIQUES 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 H41 DC A 2 N3 DC B 2 1.43 REMARK 500 O4 DT A 7 H3 DT B 7 1.54 REMARK 500 N3 DC A 2 H41 DC B 2 1.54 REMARK 500 H3 DT A 7 O4 DT B 7 1.58 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 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 5 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT B 3 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC B 4 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA B 5 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA B 5 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC B 6 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT B 7 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC B 8 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Q2T RELATED DB: PDB REMARK 900 I-MOTIF STRUCTUREWITHCOMPARABLE ORGANISATION REMARK 900 RELATED ID: 1RME RELATED DB: PDB REMARK 900 I-MOTIF STRUCTUREWITHCOMPARABLE ORGANISATION DBREF 2AWV A 1 9 PDB 2AWV 2AWV 1 9 DBREF 2AWV B 1 9 PDB 2AWV 2AWV 1 9 SEQRES 1 A 9 MCY DC DT DC DA DC DT DC DC SEQRES 1 B 9 MCY DC DT DC DA DC DT DC DC MODRES 2AWV MCY A 1 DC 5-METHYL-2'-DEOXYCYTIDINE MODRES 2AWV MCY B 1 DC 5-METHYL-2'-DEOXYCYTIDINE HET MCY A 1 31 HET MCY B 1 31 HETNAM MCY 5-METHYL-2'-DEOXYCYTIDINE FORMUL 1 MCY 2(C10 H15 N3 O4) LINK O3' MCY A 1 P DC A 2 1555 1555 1.62 LINK O3' MCY B 1 P DC B 2 1555 1555 1.62 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 HETATM 1 N1 MCY A 1 -8.319 2.558 -2.601 1.00 0.00 N HETATM 2 C2 MCY A 1 -8.519 2.170 -1.300 1.00 0.00 C HETATM 3 N3 MCY A 1 -8.574 0.846 -1.044 1.00 0.00 N HETATM 4 C4 MCY A 1 -8.440 -0.065 -2.019 1.00 0.00 C HETATM 5 C5 MCY A 1 -8.257 0.330 -3.299 1.00 0.00 C HETATM 6 C6 MCY A 1 -8.195 1.637 -3.586 1.00 0.00 C HETATM 7 O2 MCY A 1 -8.640 3.009 -0.409 1.00 0.00 O HETATM 8 N4 MCY A 1 -8.425 -1.353 -1.699 1.00 0.00 N HETATM 9 C1' MCY A 1 -8.184 3.996 -2.865 1.00 0.00 C HETATM 10 C2' MCY A 1 -6.736 4.342 -3.158 1.00 0.00 C HETATM 11 C3' MCY A 1 -6.779 5.439 -4.194 1.00 0.00 C HETATM 12 C4' MCY A 1 -8.246 5.524 -4.622 1.00 0.00 C HETATM 13 O4' MCY A 1 -8.925 4.393 -4.028 1.00 0.00 O HETATM 14 O3' MCY A 1 -6.319 6.681 -3.644 1.00 0.00 O HETATM 15 C5' MCY A 1 -8.378 5.518 -6.146 1.00 0.00 C HETATM 16 O5' MCY A 1 -8.240 4.200 -6.683 1.00 0.00 O HETATM 17 C5A MCY A 1 -8.155 -0.700 -4.419 1.00 0.00 C HETATM 18 H6 MCY A 1 -8.040 1.961 -4.614 1.00 0.00 H HETATM 19 HN41 MCY A 1 -8.271 -2.051 -2.408 1.00 0.00 H HETATM 20 HN42 MCY A 1 -8.573 -1.629 -0.739 1.00 0.00 H HETATM 21 H1' MCY A 1 -8.537 4.550 -1.991 1.00 0.00 H HETATM 22 H2' MCY A 1 -6.212 3.471 -3.553 1.00 0.00 H HETATM 23 H2'' MCY A 1 -6.244 4.699 -2.256 1.00 0.00 H HETATM 24 H3' MCY A 1 -6.163 5.154 -5.051 1.00 0.00 H HETATM 25 H4' MCY A 1 -8.680 6.441 -4.229 1.00 0.00 H HETATM 26 H5' MCY A 1 -9.357 5.917 -6.423 1.00 0.00 H HETATM 27 H5'' MCY A 1 -7.604 6.157 -6.571 1.00 0.00 H HETATM 28 HO5' MCY A 1 -8.597 4.215 -7.574 1.00 0.00 H HETATM 29 H5A1 MCY A 1 -7.781 -1.641 -4.018 1.00 0.00 H HETATM 30 H5A2 MCY A 1 -7.472 -0.336 -5.188 1.00 0.00 H HETATM 31 H5A3 MCY A 1 -9.141 -0.859 -4.856 1.00 0.00 H