HEADER DNA 24-MAY-94 177D TITLE SOLUTION STRUCTURE AND HYDRATION PATTERNS OF A PYRIMIDINE(DOT) TITLE 2 PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING A NOVEL T(DOT)CG TRIPLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*GP*AP*AP*CP*AP*GP*GP*TP*TP*TP*TP*T*CP*CP*TP*GP*TP*TP*CP*TP*TP*TP*T COMPND 4 P*T*CP*TP*TP*TP*TP*CP*C)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, TRIPLEX EXPDTA SOLUTION NMR NUMMDL 6 AUTHOR I.RADHAKRISHNAN,D.J.PATEL REVDAT 5 22-MAY-24 177D 1 REMARK REVDAT 4 16-FEB-22 177D 1 REMARK REVDAT 3 24-FEB-09 177D 1 VERSN REVDAT 2 01-APR-03 177D 1 JRNL REVDAT 1 15-OCT-94 177D 0 JRNL AUTH I.RADHAKRISHNAN,D.J.PATEL JRNL TITL SOLUTION STRUCTURE AND HYDRATION PATTERNS OF A JRNL TITL 2 PYRIMIDINE.PURINE.PYRIMIDINE DNA TRIPLEX CONTAINING A NOVEL JRNL TITL 3 T.CG BASE-TRIPLE. JRNL REF J.MOL.BIOL. V. 241 600 1994 JRNL REFN ISSN 0022-2836 JRNL PMID 8057381 JRNL DOI 10.1006/JMBI.1994.1534 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: NUMBER OF NUCLEIC ACID ATOMS -- 415 REMARK 3 RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE CONDUCTED ON REMARK 3 IDEALIZED A'- AND B-FORM STARTING STRUCTURES. ONLY THE TRIPLEX REMARK 3 REGION IN THE SEQUENCE WAS CONSIDERED. SIX STRUCTURES WERE REMARK 3 CALCULATED INITIALLY USING DISTANCE RESTRAINTS. A MAJORITY OF REMARK 3 THE DISTANCE RESTRAINTS WERE SUBSEQUENTLY REPLACED BY NOE REMARK 3 INTENSITY RESTRAINTS. THE R(1/6) VALUE WAS MONITORED DURING THE REMARK 3 REFINEMENTS. EACH STRUCTURE WAS SUBJECTED TO 500 CYCLES OF REMARK 3 ENERGY MINIMIZATION AFTER THE DYNAMICS. NO AVERAGE STRUCTURE WAS REMARK 3 CALCULATED. THE R(1/6) VALUE FOR THE MINIMIZED STRUCTURE REMARK 3 REPRESENTING THE ENSEMBLE IS 0.024. THE DYNAMICS SIMULATIONS REMARK 3 WERE PERFORMED IN THE PRESENCE OF EXPLICIT SOLVENT MOLECULES AND REMARK 3 15 NA+ COUNTER IONS. THE SUMMATION EXTENDS THROUGH ALL REMARK 3 ASSIGNABLE, QUANTIFIABLE CROSS PEAK INTENSITIES IN NOESY SPECTRA REMARK 3 RECORDED AT MIXING TIMES OF 40, 90 AND 150 MS. RMS DEVIATIONS REMARK 3 FROM IDEALIZED GEOMETRY FOR THE MINIMIZED STRUCTURE `RM' REMARK 3 REPRESENTING THE ENSEMBLE ARE AS FOLLOWS: RM BOND (ANGSTROMS) REMARK 3 0.016 (0.016) ANGLES (DEGREES) 3.825 (3.734) IMPROPERS (DEGREES) REMARK 3 0.552 (0.391) THE VALUES IN PARENTHESES CORRESPOND TO THE REMARK 3 AVERAGE VALUES FOR THE ENSEMBLE OF SIX STRUCTURES. REMARK 4 REMARK 4 177D 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_1000170171. 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 : MOLECULAR DYNAMICS, DISTANCE REMARK 210 GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 6 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 6 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: 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 1-6 REMARK 465 RES C SSSEQI REMARK 465 DT A -15 REMARK 465 DT A -16 REMARK 465 DT A -17 REMARK 465 DT A -18 REMARK 465 DT A 0 REMARK 465 DT A -10 REMARK 465 DT A -11 REMARK 465 DT A -12 REMARK 465 DT A -13 REMARK 465 DT A -14 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 1-6 REMARK 470 RES CSSEQI ATOMS REMARK 470 DC A 1 P OP1 OP2 REMARK 470 DC A 15 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 DG A 8 N1 DG A 8 C2 -0.095 REMARK 500 1 DG A 8 C4 DG A 8 C5 0.085 REMARK 500 1 DG A 8 N7 DG A 8 C8 0.064 REMARK 500 1 DA A 9 C4 DA A 9 C5 0.075 REMARK 500 1 DA A 9 C6 DA A 9 N1 -0.042 REMARK 500 1 DA A 9 N7 DA A 9 C8 0.044 REMARK 500 1 DA A 10 C4 DA A 10 C5 0.071 REMARK 500 1 DA A 10 N7 DA A 10 C8 0.045 REMARK 500 1 DC A 11 C5' DC A 11 C4' 0.049 REMARK 500 1 DC A 11 N1 DC A 11 C6 -0.046 REMARK 500 1 DC A 11 N3 DC A 11 C4 -0.057 REMARK 500 1 DC A 11 C4 DC A 11 C5 -0.064 REMARK 500 1 DA A 12 C4 DA A 12 C5 0.072 REMARK 500 1 DG A 13 N1 DG A 13 C2 -0.093 REMARK 500 1 DG A 13 C4 DG A 13 C5 0.089 REMARK 500 1 DG A 13 N7 DG A 13 C8 0.075 REMARK 500 1 DG A 14 N1 DG A 14 C2 -0.097 REMARK 500 1 DG A 14 C4 DG A 14 C5 0.092 REMARK 500 1 DG A 14 N7 DG A 14 C8 0.056 REMARK 500 1 DC A 1 N3 DC A 1 C4 -0.062 REMARK 500 1 DC A 1 C4 DC A 1 C5 -0.056 REMARK 500 1 DC A 1 C5 DC A 1 C6 0.050 REMARK 500 1 DC A 2 N1 DC A 2 C6 -0.053 REMARK 500 1 DC A 2 N3 DC A 2 C4 -0.059 REMARK 500 1 DC A 2 C4 DC A 2 C5 -0.051 REMARK 500 1 DT A 3 C2 DT A 3 N3 -0.085 REMARK 500 1 DT A 3 N3 DT A 3 C4 -0.080 REMARK 500 1 DT A 3 C4 DT A 3 C5 0.081 REMARK 500 1 DT A 3 C5 DT A 3 C6 0.051 REMARK 500 1 DT A 3 C6 DT A 3 N1 -0.051 REMARK 500 1 DG A 4 N1 DG A 4 C2 -0.106 REMARK 500 1 DG A 4 C4 DG A 4 C5 0.089 REMARK 500 1 DG A 4 N7 DG A 4 C8 0.046 REMARK 500 1 DG A 4 C8 DG A 4 N9 -0.046 REMARK 500 1 DT A 5 C2 DT A 5 N3 -0.078 REMARK 500 1 DT A 5 N3 DT A 5 C4 -0.074 REMARK 500 1 DT A 5 C4 DT A 5 C5 0.077 REMARK 500 1 DT A 5 C5 DT A 5 C6 0.045 REMARK 500 1 DT A 5 C6 DT A 5 N1 -0.045 REMARK 500 1 DT A 6 C2 DT A 6 N3 -0.076 REMARK 500 1 DT A 6 N3 DT A 6 C4 -0.077 REMARK 500 1 DT A 6 C4 DT A 6 C5 0.087 REMARK 500 1 DT A 6 C5 DT A 6 C6 0.056 REMARK 500 1 DT A 6 C6 DT A 6 N1 -0.046 REMARK 500 1 DC A 7 N1 DC A 7 C6 -0.042 REMARK 500 1 DC A 7 N3 DC A 7 C4 -0.068 REMARK 500 1 DC A 7 C4 DC A 7 C5 -0.066 REMARK 500 1 DC A 7 C5 DC A 7 C6 0.059 REMARK 500 1 DC A 15 N3 DC A 15 C4 -0.073 REMARK 500 1 DC A 15 C5 DC A 15 C6 0.060 REMARK 500 REMARK 500 THIS ENTRY HAS 460 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 DG A 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG A 8 C2 - N3 - C4 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DG A 8 N3 - C4 - C5 ANGL. DEV. = -7.3 DEGREES REMARK 500 1 DG A 8 C5 - C6 - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DG A 8 N3 - C4 - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DG A 8 C6 - C5 - N7 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG A 8 N3 - C2 - N2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 8 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA A 9 O3' - P - O5' ANGL. DEV. = 11.4 DEGREES REMARK 500 1 DA A 9 OP1 - P - OP2 ANGL. DEV. = -11.1 DEGREES REMARK 500 1 DA A 9 N1 - C2 - N3 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DA A 9 C2 - N3 - C4 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DA A 9 C4 - C5 - C6 ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DA A 9 C5 - C6 - N1 ANGL. DEV. = 8.0 DEGREES REMARK 500 1 DA A 9 C6 - C5 - N7 ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DA A 9 N1 - C6 - N6 ANGL. DEV. = -9.6 DEGREES REMARK 500 1 DA A 10 O3' - P - O5' ANGL. DEV. = 13.7 DEGREES REMARK 500 1 DA A 10 OP1 - P - OP2 ANGL. DEV. = -11.9 DEGREES REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = -8.3 DEGREES REMARK 500 1 DA A 10 C2 - N3 - C4 ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DA A 10 N3 - C4 - C5 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DA A 10 C4 - C5 - C6 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DA A 10 C5 - C6 - N1 ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DA A 10 C6 - C5 - N7 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DA A 10 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC A 11 O3' - P - O5' ANGL. DEV. = 12.6 DEGREES REMARK 500 1 DC A 11 OP1 - P - OP2 ANGL. DEV. = -11.0 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC A 11 N3 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC A 11 N1 - C2 - O2 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DA A 12 O3' - P - O5' ANGL. DEV. = 14.3 DEGREES REMARK 500 1 DA A 12 OP1 - P - OP2 ANGL. DEV. = -10.8 DEGREES REMARK 500 1 DA A 12 N1 - C2 - N3 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DA A 12 C2 - N3 - C4 ANGL. DEV. = 7.1 DEGREES REMARK 500 1 DA A 12 N3 - C4 - C5 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DA A 12 C4 - C5 - C6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA A 12 C5 - C6 - N1 ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DA A 12 N3 - C4 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DA A 12 C6 - C5 - N7 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DA A 12 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG A 13 O3' - P - O5' ANGL. DEV. = 12.0 DEGREES REMARK 500 1 DG A 13 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 1 DG A 13 C2 - N3 - C4 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DG A 13 N3 - C4 - C5 ANGL. DEV. = -7.0 DEGREES REMARK 500 1 DG A 13 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 13 N3 - C4 - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DG A 13 C6 - C5 - N7 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 13 N3 - C2 - N2 ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DG A 14 O3' - P - O5' ANGL. DEV. = 11.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 789 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 177D A 8 21 PDB 177D 177D 8 21 SEQRES 1 A 31 DG DA DA DC DA DG DG DT DT DT DT DT DC SEQRES 2 A 31 DC DT DG DT DT DC DT DT DT DT DT DC DT SEQRES 3 A 31 DT DT 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