HEADER DNA 30-AUG-93 136D TITLE SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE TITLE 2 DNA TRIPLEX CONTAINING G(DOT)GC AND T(DOT)AT TRIPLES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA TRIPLEX; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, NMR, TRIPLEX EXPDTA SOLUTION NMR NUMMDL 14 AUTHOR I.RADHAKRISHNAN,D.J.PATEL REVDAT 3 24-FEB-09 136D 1 VERSN REVDAT 2 01-APR-03 136D 1 JRNL REVDAT 1 30-APR-94 136D 0 JRNL AUTH I.RADHAKRISHNAN,D.J.PATEL JRNL TITL SOLUTION STRUCTURE OF A PURINE.PURINE.PYRIMIDINE JRNL TITL 2 DNA TRIPLEX CONTAINING G.GC AND T.AT TRIPLES. JRNL REF STRUCTURE V. 1 135 1993 JRNL REFN ISSN 0969-2126 JRNL PMID 8069626 JRNL DOI 10.1016/0969-2126(93)90028-F REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.RADHAKRISHNAN,D.J.PATEL REMARK 1 TITL SOLUTION STRUCTURE OF AN INTRAMOLECULAR REMARK 1 TITL 2 PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX REMARK 1 REF J.AM.CHEM.SOC. V. 115 1615 1993 REMARK 1 REFN ISSN 0002-7863 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: RESTRAINED MOLECULAR DYNAMICS REMARK 3 CALCULATIONS WERE DONE ON IDEALIZED A'- AND B-FORM STARTING REMARK 3 STRUCTURES. ONLY THE TRIPLEX REGION AND THE FIRST AND LAST REMARK 3 RESIDUES OF EACH OF THE TWO LOOPS IN THE SEQUENCE WERE REMARK 3 CONSIDERED. THE REFINEMENT WAS CONDUCTED IN TWO STAGES. IN THE REMARK 3 FIRST STAGE, SIX STRUCTURES WERE CALCULATED (THREE FROM EACH REMARK 3 STARTING STRUCTURE) USING DISTANCE RESTRAINTS. IN THE SECOND REMARK 3 STAGE, TWO OF THE SIX STRUCTURES WERE REFINED DIRECTLY AGAINST REMARK 3 PRIMARY NOE DATA. THE R(1/6) VALUE WAS USED TO MONITOR THE REMARK 3 REFINEMENT DURING THIS STAGE. THE FINAL R(1/6) VALUES FOR THE REMARK 3 TWO AVERAGED MINIMIZED STRUCTURES WERE 0.04 AND 0.045. THE REMARK 3 SUMMATION RUNS THROUGH ALL OBSERVED, QUANTIFIABLE CROSSPEAK REMARK 3 INTENSITIES IN NOESY SPECTRA RECORDED AT MIXING TIMES OF 40, REMARK 3 90 AND 150 MS. RMSD BOND DISTANCES 0.016 ANGSTROMS RMSD BOND REMARK 3 ANGLES 3.96 DEGREES RMS DEVIATIONS FROM IDEALIZED GEOMETRY FOR REMARK 3 THE TWO AVERAGED MINIMIZED STRUCTURES ARE AS FOLLOWS: < REMARK 3 RM-B> BOND (ANGSTROMS) 0.016 0.018 ANGLES (DEGREES) 3.959 REMARK 3 4.212 IMPROPERS (DEGREES) 0.433 0.472 REMARK 4 REMARK 4 136D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. 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 : RESTRAINED MOLECULAR REMARK 210 DYNAMICS, DISTANCE GEOMETRY 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: STRUCTURE ANALYSES WERE CONDUCTED ON SIXTEEN STRUCTURES REMARK 210 INCLUDING FOURTEEN STRUCTURES TAKEN FROM THE RESTRAINED REMARK 210 MOLECULAR DYNAMICS TRAJECTORIES OF THE TWO REFINEMENTS, AND REMARK 210 THE TWO AVERAGED MINIMIZED STRUCTURES. THE COORDINATES FOR THE REMARK 210 TWO AVERAGED MINIMIZED STRUCTURES CAN BE FOUND IN PROTEIN DATA REMARK 210 BANK ENTRIES 134D AND 135D, RESPECTIVELY. THE COORDINATES FOR REMARK 210 THE 14 STRUCTURES FROM THE RESTRAINED MOLECULAR DYNAMICS REMARK 210 TRAJECTORIES CAN BE FOUND IN ENTRY 136D. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-14 REMARK 465 RES C SSSEQI REMARK 465 DT A 2L REMARK 465 DT A 3L REMARK 465 DT A 4L REMARK 465 DT A 7L REMARK 465 DT A 8L REMARK 465 DT A 9L REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-14 REMARK 470 RES CSSEQI ATOMS REMARK 470 DT A 5L P OP1 OP2 REMARK 470 DT A 10L P OP1 OP2 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 DT A 1 C5' DT A 1 C4' 0.048 REMARK 500 1 DT A 1 C3' DT A 1 C2' 0.129 REMARK 500 1 DT A 1 C2' DT A 1 C1' 0.075 REMARK 500 1 DT A 1 N3 DT A 1 C4 -0.070 REMARK 500 1 DT A 1 C5 DT A 1 C7 0.065 REMARK 500 1 DC A 2 N1 DC A 2 C6 0.042 REMARK 500 1 DC A 2 C5 DC A 2 C6 0.061 REMARK 500 1 DC A 2 O3' DC A 3 P 0.089 REMARK 500 1 DT A 4 O4' DT A 4 C4' -0.067 REMARK 500 1 DT A 4 C2 DT A 4 N3 -0.062 REMARK 500 1 DT A 4 N3 DT A 4 C4 0.055 REMARK 500 1 DT A 4 C5 DT A 4 C6 0.049 REMARK 500 1 DC A 5 C5' DC A 5 C4' 0.080 REMARK 500 1 DC A 5 C4 DC A 5 C5 -0.049 REMARK 500 1 DC A 6 C4 DC A 6 N4 -0.056 REMARK 500 1 DT A 7 P DT A 7 O5' 0.064 REMARK 500 1 DT A 7 C5 DT A 7 C6 0.058 REMARK 500 1 DT A 1L P DT A 1L O5' 0.078 REMARK 500 1 DT A 1L N1 DT A 1L C2 0.058 REMARK 500 1 DT A 1L C5 DT A 1L C6 0.055 REMARK 500 1 DT A 1L C5 DT A 1L C7 0.097 REMARK 500 1 DT A 5L C2' DT A 5L C1' 0.087 REMARK 500 1 DT A 5L C5 DT A 5L C6 0.083 REMARK 500 1 DA A 8 C5' DA A 8 C4' 0.068 REMARK 500 1 DA A 8 C3' DA A 8 C2' 0.129 REMARK 500 1 DA A 8 C2' DA A 8 C1' 0.102 REMARK 500 1 DA A 8 C6 DA A 8 N1 -0.043 REMARK 500 1 DA A 8 N7 DA A 8 C8 -0.058 REMARK 500 1 DG A 9 C4' DG A 9 C3' 0.074 REMARK 500 1 DG A 9 C2' DG A 9 C1' 0.079 REMARK 500 1 DG A 9 C2 DG A 9 N3 0.093 REMARK 500 1 DG A 9 N3 DG A 9 C4 0.045 REMARK 500 1 DG A 9 C6 DG A 9 N1 0.044 REMARK 500 1 DG A 10 O4' DG A 10 C4' 0.056 REMARK 500 1 DG A 10 C5 DG A 10 N7 -0.057 REMARK 500 1 DA A 11 C3' DA A 11 C2' 0.096 REMARK 500 1 DG A 13 P DG A 13 O5' 0.069 REMARK 500 1 DG A 13 C5' DG A 13 C4' 0.051 REMARK 500 1 DG A 13 O4' DG A 13 C1' 0.071 REMARK 500 1 DG A 13 N1 DG A 13 C2 -0.059 REMARK 500 1 DA A 14 C3' DA A 14 C2' 0.080 REMARK 500 1 DA A 14 C2' DA A 14 C1' 0.108 REMARK 500 1 DA A 14 O4' DA A 14 C4' 0.086 REMARK 500 1 DA A 14 N3 DA A 14 C4 0.063 REMARK 500 1 DA A 14 N7 DA A 14 C8 0.050 REMARK 500 1 DT A 6L C5' DT A 6L C4' 0.065 REMARK 500 1 DT A 6L C2' DT A 6L C1' 0.110 REMARK 500 1 DT A 6L N3 DT A 6L C4 -0.077 REMARK 500 1 DT A 6L C5 DT A 6L C7 -0.049 REMARK 500 1 DT A 10L C5' DT A 10L C4' 0.060 REMARK 500 REMARK 500 THIS ENTRY HAS 1089 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 DT A 1 C5' - C4' - O4' ANGL. DEV. = 9.0 DEGREES REMARK 500 1 DT A 1 O4' - C1' - C2' ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DT A 1 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DT A 1 N1 - C2 - O2 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DT A 1 N3 - C2 - O2 ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DT A 1 N3 - C4 - O4 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DT A 1 C5 - C4 - O4 ANGL. DEV. = -6.7 DEGREES REMARK 500 1 DC A 2 C4' - C3' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 1 DC A 2 O4' - C1' - C2' ANGL. DEV. = -8.3 DEGREES REMARK 500 1 DC A 2 C5 - C6 - N1 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DC A 2 N1 - C2 - O2 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DC A 2 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DC A 2 N3 - C4 - N4 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DC A 3 C1' - O4' - C4' ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DC A 3 N3 - C4 - C5 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC A 3 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DC A 3 C6 - N1 - C1' ANGL. DEV. = 8.5 DEGREES REMARK 500 1 DC A 3 C2 - N1 - C1' ANGL. DEV. = -6.9 DEGREES REMARK 500 1 DC A 2 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES REMARK 500 1 DT A 4 O4' - C1' - C2' ANGL. DEV. = -8.5 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 15.3 DEGREES REMARK 500 1 DT A 4 N1 - C2 - N3 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT A 4 N3 - C2 - O2 ANGL. DEV. = -6.9 DEGREES REMARK 500 1 DT A 4 C4 - C5 - C7 ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -7.5 DEGREES REMARK 500 1 DC A 5 O4' - C4' - C3' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC A 5 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 5 C5 - C6 - N1 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DC A 5 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DC A 5 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DC A 5 C2 - N1 - C1' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DC A 6 C1' - O4' - C4' ANGL. DEV. = -9.2 DEGREES REMARK 500 1 DC A 6 C2 - N3 - C4 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DC A 6 N1 - C2 - O2 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DT A 7 C1' - O4' - C4' ANGL. DEV. = -8.9 DEGREES REMARK 500 1 DT A 7 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DT A 7 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT A 7 C5 - C6 - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT A 7 N3 - C4 - O4 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DT A 7 C5 - C4 - O4 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DT A 7 C4 - C5 - C7 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -9.3 DEGREES REMARK 500 1 DT A 1L O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DT A 1L O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT A 1L C2 - N3 - C4 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 1L C5 - C6 - N1 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DT A 1L C6 - C5 - C7 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DT A 5L O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1805 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 2 DC A 3 0.07 SIDE_CHAIN REMARK 500 4 DC A 3 0.07 SIDE_CHAIN REMARK 500 8 DT A 6L 0.07 SIDE_CHAIN REMARK 500 10 DC A 3 0.06 SIDE_CHAIN REMARK 500 11 DC A 3 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 134D RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE REMARK 900 RELATED ID: 135D RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE DBREF 136D A 1 21 PDB 136D 136D 1 21 SEQRES 1 A 31 DT DC DC DT DC DC DT DT DT DT DT DT DA SEQRES 2 A 31 DG DG DA DG DG DA DT DT DT DT DT DT DG SEQRES 3 A 31 DG DT DG DG DT 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 ENDMDL ENDMDL ENDMDL ENDMDL MASTER 262 0 0 0 0 0 0 6 0 0 0 3 END