HEADER DNA 15-NOV-93 149D TITLE SOLUTION STRUCTURE OF A PYRIMIDINE(DOT)PURINE(DOT) PYRIMIDINE DNA TITLE 2 TRIPLEX CONTAINING T(DOT)AT, C+(DOT)GC AND G(DOT)TA TRIPLES COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*TP*AP*TP*TP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*AP*AP*TP*AP*GP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(*CP*TP*TP*GP*TP*CP*C)-3'; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 MOL_ID: 3; SOURCE 7 SYNTHETIC: YES KEYWDS DNA, TRIPLEX EXPDTA SOLUTION NMR NUMMDL 14 AUTHOR I.RADHAKRISHNAN,D.J.PATEL REVDAT 5 22-MAY-24 149D 1 REMARK REVDAT 4 16-FEB-22 149D 1 REMARK REVDAT 3 24-FEB-09 149D 1 VERSN REVDAT 2 01-APR-03 149D 1 JRNL REVDAT 1 30-APR-94 149D 0 JRNL AUTH I.RADHAKRISHNAN,D.J.PATEL JRNL TITL SOLUTION STRUCTURE OF A PYRIMIDINE.PURINE.PYRIMIDINE DNA JRNL TITL 2 TRIPLEX CONTAINING T.AT, C+.GC AND G.TA TRIPLES. JRNL REF STRUCTURE V. 2 17 1994 JRNL REFN ISSN 0969-2126 JRNL PMID 8075980 JRNL DOI 10.1016/S0969-2126(00)00005-8 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.RADHAKRISHNAN,D.J.PATEL,X.GAO REMARK 1 TITL THREE-DIMENSIONAL HOMONUCLEAR NOESY-TOCSY OF AN REMARK 1 TITL 2 INTRAMOLECULAR PYRIMIDINE(DOT)PURINE(DOT)PYRIMIDINE DNA REMARK 1 TITL 3 TRIPLEX CONTAINING A CENTRAL G(DOT)TA TRIPLE: REMARK 1 TITL 4 NONEXCHANGEABLE PROTON ASSIGNMENTS AND STRUCTURAL REMARK 1 TITL 5 IMPLICATIONS REMARK 1 REF BIOCHEMISTRY V. 31 2514 1992 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH I.RADHAKRISHNAN,D.J.PATEL,J.M.VEAL,X.GAO REMARK 1 TITL SOLUTION CONFORMATION OF A G(DOT)TA TRIPLE IN AN REMARK 1 TITL 2 INTRAMOLECULAR PYRIMIDINE(DOT)PURINE(DOT)PYRIMIDINE DNA REMARK 1 TITL 3 TRIPLEX REMARK 1 REF J.AM.CHEM.SOC. V. 114 6913 1992 REMARK 1 REFN ISSN 0002-7863 REMARK 1 REFERENCE 3 REMARK 1 AUTH I.RADHAKRISHNAN,X.GAO,C.DE LOS SANTOS,D.LIVE,D.J.PATEL REMARK 1 TITL NMR STRUCTURAL STUDIES OF INTRAMOLECULAR REMARK 1 TITL 2 (Y+)N(DOT)(R+)N(Y-)N DNA TRIPLEXES IN SOLUTION: IMINO AND REMARK 1 TITL 3 AMINO PROTON AND NITROGEN MARKERS OF G(DOT)TA BASE TRIPLE REMARK 1 TITL 4 FORMATION REMARK 1 REF BIOCHEMISTRY V. 30 9022 1991 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: R VALUE 0.022 RMSD BOND DISTANCES 0.005 REMARK 3 ANGSTROMS RMSD BOND ANGLES 2.26 DEGREES REMARK 4 REMARK 4 149D 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_1000170111. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 14 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 1 DC A 1 N1 DC A 1 C6 -0.042 REMARK 500 1 DC A 1 N3 DC A 1 C4 -0.065 REMARK 500 1 DC A 1 C4 DC A 1 C5 -0.065 REMARK 500 1 DC A 1 C5 DC A 1 C6 0.055 REMARK 500 1 DC A 2 N1 DC A 2 C6 -0.045 REMARK 500 1 DC A 2 N3 DC A 2 C4 -0.055 REMARK 500 1 DC A 2 C4 DC A 2 C5 -0.052 REMARK 500 1 DC A 2 C5 DC A 2 C6 0.050 REMARK 500 1 DT A 3 C2 DT A 3 N3 -0.093 REMARK 500 1 DT A 3 N3 DT A 3 C4 -0.087 REMARK 500 1 DT A 3 C4 DT A 3 C5 0.092 REMARK 500 1 DT A 3 C5 DT A 3 C6 0.053 REMARK 500 1 DT A 3 C6 DT A 3 N1 -0.045 REMARK 500 1 DA A 4 C4 DA A 4 C5 0.067 REMARK 500 1 DA A 4 N7 DA A 4 C8 0.047 REMARK 500 1 DT A 5 C2 DT A 5 N3 -0.085 REMARK 500 1 DT A 5 N3 DT A 5 C4 -0.082 REMARK 500 1 DT A 5 C4 DT A 5 C5 0.090 REMARK 500 1 DT A 5 C5 DT A 5 C6 0.055 REMARK 500 1 DT A 6 P DT A 6 O5' -0.063 REMARK 500 1 DT A 6 C2 DT A 6 N3 -0.078 REMARK 500 1 DT A 6 N3 DT A 6 C4 -0.086 REMARK 500 1 DT A 6 C4 DT A 6 C5 0.088 REMARK 500 1 DT A 6 C5 DT A 6 C6 0.047 REMARK 500 1 DT A 6 C6 DT A 6 N1 -0.055 REMARK 500 1 DC A 7 N1 DC A 7 C6 -0.055 REMARK 500 1 DC A 7 N3 DC A 7 C4 -0.059 REMARK 500 1 DC A 7 C4 DC A 7 C5 -0.048 REMARK 500 1 DC A 7 C5 DC A 7 C6 0.052 REMARK 500 1 DG B 8 N1 DG B 8 C2 -0.098 REMARK 500 1 DG B 8 C4 DG B 8 C5 0.092 REMARK 500 1 DG B 8 N7 DG B 8 C8 0.056 REMARK 500 1 DA B 9 C4 DA B 9 C5 0.081 REMARK 500 1 DA B 9 N7 DA B 9 C8 0.053 REMARK 500 1 DA B 10 C4 DA B 10 C5 0.082 REMARK 500 1 DA B 10 N7 DA B 10 C8 0.044 REMARK 500 1 DT B 11 C2 DT B 11 N3 -0.098 REMARK 500 1 DT B 11 N3 DT B 11 C4 -0.081 REMARK 500 1 DT B 11 C4 DT B 11 C5 0.071 REMARK 500 1 DT B 11 C5 DT B 11 C6 0.058 REMARK 500 1 DT B 11 C6 DT B 11 N1 -0.042 REMARK 500 1 DA B 12 C4 DA B 12 C5 0.077 REMARK 500 1 DA B 12 N7 DA B 12 C8 0.062 REMARK 500 1 DG B 13 P DG B 13 O5' -0.077 REMARK 500 1 DG B 13 N1 DG B 13 C2 -0.101 REMARK 500 1 DG B 13 C4 DG B 13 C5 0.091 REMARK 500 1 DG B 13 N7 DG B 13 C8 0.079 REMARK 500 1 DG B 14 N1 DG B 14 C2 -0.099 REMARK 500 1 DG B 14 C4 DG B 14 C5 0.094 REMARK 500 1 DG B 14 N7 DG B 14 C8 0.056 REMARK 500 REMARK 500 THIS ENTRY HAS 1005 BOND DEVIATIONS. 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 OP1 - P - OP2 ANGL. DEV. = -11.5 DEGREES REMARK 500 1 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 3 O3' - P - O5' ANGL. DEV. = 11.5 DEGREES REMARK 500 1 DT A 3 OP1 - P - OP2 ANGL. DEV. = -9.6 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 3 N1 - C2 - N3 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DT A 3 C5 - C6 - N1 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 3 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DT A 3 C4 - C5 - C7 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DA A 4 OP1 - P - OP2 ANGL. DEV. = -9.9 DEGREES REMARK 500 1 DA A 4 N1 - C2 - N3 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA A 4 C2 - N3 - C4 ANGL. DEV. = 8.0 DEGREES REMARK 500 1 DA A 4 N3 - C4 - C5 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA A 4 C4 - C5 - C6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DA A 4 C5 - C6 - N1 ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DA A 4 N3 - C4 - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DA A 4 C6 - C5 - N7 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DT A 5 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES REMARK 500 1 DT A 5 N1 - C2 - N3 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DT A 5 C5 - C6 - N1 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT A 5 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DT A 5 C4 - C5 - C7 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DT A 6 N1 - C2 - N3 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DT A 6 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DT A 6 C4 - C5 - C7 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DC A 7 OP1 - P - OP2 ANGL. DEV. = -11.2 DEGREES REMARK 500 1 DC A 7 N1 - C2 - O2 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DC A 7 N3 - C2 - O2 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DG B 8 C2 - N3 - C4 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DG B 8 N3 - C4 - C5 ANGL. DEV. = -7.8 DEGREES REMARK 500 1 DG B 8 C5 - C6 - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG B 8 N3 - C4 - N9 ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DG B 8 C6 - C5 - N7 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG B 8 N1 - C6 - O6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DA B 9 OP1 - P - OP2 ANGL. DEV. = -11.0 DEGREES REMARK 500 1 DA B 9 C2 - N3 - C4 ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DA B 9 N3 - C4 - C5 ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DA B 9 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA B 9 C5 - C6 - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 1 DA B 9 N3 - C4 - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DA B 9 C6 - C5 - N7 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DA B 9 N1 - C6 - N6 ANGL. DEV. = -8.0 DEGREES REMARK 500 1 DA B 10 OP1 - P - OP2 ANGL. DEV. = -9.9 DEGREES REMARK 500 1 DA B 10 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DA B 10 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DA B 10 N1 - C2 - N3 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA B 10 C2 - N3 - C4 ANGL. DEV. = 6.6 DEGREES REMARK 500 1 DA B 10 N3 - C4 - C5 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DA B 10 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1879 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 149D A 1 7 PDB 149D 149D 1 7 DBREF 149D B 8 14 PDB 149D 149D 8 14 DBREF 149D C 15 21 PDB 149D 149D 15 21 SEQRES 1 A 7 DC DC DT DA DT DT DC SEQRES 1 B 7 DG DA DA DT DA DG DG SEQRES 1 C 7 DC DT DT DG DT DC DC 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