HEADER DNA 15-JUL-98 1C11 TITLE INTERCALATED D(TCCCGTTTCCA) DIMER, NMR, 7 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*CP*CP*CP*GP*TP*TP*TP*CP*CP*A)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS ALPHOID DNA, CENTROMERE, HAIRPIN, I-MOTIF EXPDTA SOLUTION NMR NUMMDL 7 AUTHOR J.GALLEGO,S.H.CHOU,B.R.REID REVDAT 3 24-FEB-09 1C11 1 VERSN REVDAT 2 22-DEC-99 1C11 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 22-JUL-98 1C11 0 JRNL AUTH J.GALLEGO,S.H.CHOU,B.R.REID JRNL TITL CENTROMERIC PYRIMIDINE STRANDS FOLD INTO AN JRNL TITL 2 INTERCALATED MOTIF BY FORMING A DOUBLE HAIRPIN JRNL TITL 3 WITH A NOVEL T:G:G:T TETRAD: SOLUTION STRUCTURE OF JRNL TITL 4 THE D(TCCCGTTTCCA) DIMER. JRNL REF J.MOL.BIOL. V. 273 840 1997 JRNL REFN ISSN 0022-2836 JRNL PMID 9367776 JRNL DOI 10.1006/JMBI.1997.1361 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BIRDER REMARK 3 AUTHORS : ZHU & REID REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED NOESY BACK-CALCULATION (BIRDER) REMARK 3 ; DISTANCE GEOMETRY (DGII) AND MOLECULAR DYNAMICS (DISCOVER, REMARK 3 AMBER) REMARK 4 REMARK 4 1C11 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-SEP-99. REMARK 100 THE RCSB ID CODE IS RCSB008177. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 302 REMARK 210 PH : 4.1 REMARK 210 IONIC STRENGTH : 0.2M REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D H/H NOESY, H/H COSY, H/P REMARK 210 HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 750 MHZ REMARK 210 SPECTROMETER MODEL : HOME-BUILT, DMX-750 REMARK 210 SPECTROMETER MANUFACTURER : HOME-BUILT, BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX, BIRDER, DGII, REMARK 210 DISCOVER, AMBER REMARK 210 METHOD USED : NOESY BACKC.+DG+MD REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 7 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURE CONVERGENCE 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 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 1 DC A 2 N3 DC A 2 C4 0.044 REMARK 500 1 DC A 3 N3 DC A 3 C4 0.042 REMARK 500 1 DC A 4 N3 DC A 4 C4 0.046 REMARK 500 1 DC A 10 N3 DC A 10 C4 0.044 REMARK 500 1 DA A 11 C5' DA A 11 C4' 0.046 REMARK 500 1 DA B 11 C5' DA B 11 C4' 0.045 REMARK 500 2 DC A 2 N3 DC A 2 C4 0.045 REMARK 500 2 DC A 4 N3 DC A 4 C4 0.044 REMARK 500 2 DC A 10 N3 DC A 10 C4 0.045 REMARK 500 3 DC A 2 N3 DC A 2 C4 0.045 REMARK 500 3 DC A 4 N3 DC A 4 C4 0.046 REMARK 500 3 DC A 10 N3 DC A 10 C4 0.044 REMARK 500 4 DC A 2 N3 DC A 2 C4 0.044 REMARK 500 4 DC A 4 N3 DC A 4 C4 0.046 REMARK 500 4 DC A 10 N3 DC A 10 C4 0.044 REMARK 500 4 DA B 11 C5' DA B 11 C4' 0.046 REMARK 500 5 DC A 2 N3 DC A 2 C4 0.044 REMARK 500 5 DC A 4 N3 DC A 4 C4 0.045 REMARK 500 5 DC A 10 N3 DC A 10 C4 0.044 REMARK 500 5 DA A 11 C5' DA A 11 C4' 0.046 REMARK 500 6 DC A 2 N3 DC A 2 C4 0.043 REMARK 500 6 DC A 4 N3 DC A 4 C4 0.046 REMARK 500 6 DC A 10 N3 DC A 10 C4 0.044 REMARK 500 6 DA B 11 C5' DA B 11 C4' 0.046 REMARK 500 7 DC A 2 N3 DC A 2 C4 0.043 REMARK 500 7 DC A 4 N3 DC A 4 C4 0.046 REMARK 500 7 DC A 10 N3 DC A 10 C4 0.045 REMARK 500 7 DA A 11 C5' DA A 11 C4' 0.045 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. = 3.2 DEGREES REMARK 500 1 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DC A 3 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DC A 4 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 5 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC A 9 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DC A 10 N1 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DC B 2 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG B 5 O4' - C1' - N9 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DT B 6 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT B 7 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DC A 3 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DC A 4 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DG A 5 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = -6.5 DEGREES REMARK 500 2 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC A 9 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DC A 10 N1 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DC B 2 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC B 3 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DG B 5 O4' - C1' - N9 ANGL. DEV. = -5.9 DEGREES REMARK 500 2 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 DC A 3 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 3 DC A 3 N1 - C2 - O2 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 DC A 4 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 DG A 5 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 3 DG A 5 O4' - C1' - N9 ANGL. DEV. = -6.1 DEGREES REMARK 500 3 DT A 7 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DC A 9 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 DC A 10 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 DC B 2 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 DC B 3 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 3 DG B 5 O4' - C1' - N9 ANGL. DEV. = -6.3 DEGREES REMARK 500 3 DT B 6 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 3 DT B 7 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 4 DC A 3 N1 - C2 - O2 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 DC A 4 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 DG A 5 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 4 DG A 5 O4' - C1' - N9 ANGL. DEV. = -6.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 103 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 10 0.09 SIDE_CHAIN REMARK 500 1 DA A 11 0.07 SIDE_CHAIN REMARK 500 1 DC B 10 0.10 SIDE_CHAIN REMARK 500 1 DA B 11 0.07 SIDE_CHAIN REMARK 500 2 DC A 10 0.08 SIDE_CHAIN REMARK 500 2 DA A 11 0.07 SIDE_CHAIN REMARK 500 2 DC B 10 0.09 SIDE_CHAIN REMARK 500 2 DA B 11 0.07 SIDE_CHAIN REMARK 500 3 DC A 10 0.08 SIDE_CHAIN REMARK 500 3 DA A 11 0.06 SIDE_CHAIN REMARK 500 3 DC B 10 0.09 SIDE_CHAIN REMARK 500 3 DA B 11 0.06 SIDE_CHAIN REMARK 500 4 DC A 10 0.08 SIDE_CHAIN REMARK 500 4 DA A 11 0.07 SIDE_CHAIN REMARK 500 4 DC B 10 0.10 SIDE_CHAIN REMARK 500 4 DA B 11 0.07 SIDE_CHAIN REMARK 500 5 DC A 10 0.09 SIDE_CHAIN REMARK 500 5 DA A 11 0.06 SIDE_CHAIN REMARK 500 5 DC B 10 0.09 SIDE_CHAIN REMARK 500 5 DA B 11 0.06 SIDE_CHAIN REMARK 500 6 DC A 10 0.08 SIDE_CHAIN REMARK 500 6 DA A 11 0.06 SIDE_CHAIN REMARK 500 6 DC B 10 0.11 SIDE_CHAIN REMARK 500 6 DA B 11 0.06 SIDE_CHAIN REMARK 500 7 DC A 10 0.09 SIDE_CHAIN REMARK 500 7 DA A 11 0.06 SIDE_CHAIN REMARK 500 7 DC B 10 0.08 SIDE_CHAIN REMARK 500 7 DA B 11 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1C11 A 1 11 PDB 1C11 1C11 1 11 DBREF 1C11 B 1 11 PDB 1C11 1C11 1 11 SEQRES 1 A 11 DT DC DC DC DG DT DT DT DC DC DA SEQRES 1 B 11 DT DC DC DC DG DT DT DT DC DC DA 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 MASTER 208 0 0 0 0 0 0 6 0 0 0 2 END