HEADER DNA 30-AUG-93 136D TITLE SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX TITLE 2 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, TRIPLEX EXPDTA SOLUTION NMR NUMMDL 14 AUTHOR I.RADHAKRISHNAN,D.J.PATEL REVDAT 5 22-MAY-24 136D 1 REMARK REVDAT 4 23-MAR-22 136D 1 REMARK 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 DNA TRIPLEX JRNL TITL 2 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, 90 REMARK 3 AND 150 MS. RMSD BOND DISTANCES 0.016 ANGSTROMS RMSD BOND ANGLES REMARK 3 3.96 DEGREES RMS DEVIATIONS FROM IDEALIZED GEOMETRY FOR THE TWO REMARK 3 AVERAGED MINIMIZED STRUCTURES ARE AS FOLLOWS: BOND REMARK 3 (ANGSTROMS) 0.016 0.018 ANGLES (DEGREES) 3.959 4.212 IMPROPERS REMARK 3 (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 100 THE DEPOSITION ID IS D_1000170085. 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 DYNAMICS, REMARK 210 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 THE REMARK 210 TWO AVERAGED MINIMIZED STRUCTURES. THE COORDINATES FOR THE TWO REMARK 210 AVERAGED MINIMIZED STRUCTURES CAN BE FOUND IN PROTEIN DATA BANK REMARK 210 ENTRIES 134D AND 135D, RESPECTIVELY. THE COORDINATES FOR THE 14 REMARK 210 STRUCTURES FROM THE RESTRAINED MOLECULAR DYNAMICS TRAJECTORIES REMARK 210 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 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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: 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 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. = 4.2 DEGREES REMARK 500 1 DC A 2 C3' - O3' - P ANGL. DEV. = 9.0 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. = -7.0 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. = -5.5 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 MODEL 1