HEADER DNA 01-AUG-90 1D19 TITLE SOLUTION CONFORMATION OF PURINE-PYRIMIDINE DNA OCTAMERS TITLE 2 USING NUCLEAR MAGNETIC RESONANCE, RESTRAINED MOLECULAR TITLE 3 DYNAMICS AND NOE-BASED REFINEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*TP*AP*CP*GP*TP*AP*C)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, NMR, DOUBLE HELIX EXPDTA SOLUTION NMR AUTHOR J.D.BALEJA,B.D.SYKES REVDAT 4 24-FEB-09 1D19 1 VERSN REVDAT 3 01-APR-03 1D19 1 JRNL REVDAT 2 15-OCT-94 1D19 1 COMPND EXPDTA REVDAT 1 15-JUL-91 1D19 0 JRNL AUTH J.D.BALEJA,M.W.GERMANN,J.H.VAN DE SANDE,B.D.SYKES JRNL TITL SOLUTION CONFORMATION OF PURINE-PYRIMIDINE DNA JRNL TITL 2 OCTAMERS USING NUCLEAR MAGNETIC RESONANCE, JRNL TITL 3 RESTRAINED MOLECULAR DYNAMICS AND NOE-BASED JRNL TITL 4 REFINEMENT. JRNL REF J.MOL.BIOL. V. 215 411 1990 JRNL REFN ISSN 0022-2836 JRNL PMID 2231713 JRNL DOI 10.1016/S0022-2836(05)80361-4 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.D.BALEJA,J.MOULT,B.D.SYKES REMARK 1 TITL DISTANCE MEASUREMENT AND STRUCTURE REFINEMENT WITH REMARK 1 TITL 2 NOE DATA REMARK 1 REF J.MAGN.RESON. V. 87 375 1990 REMARK 1 REFN ISSN 0022-2364 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMOS REMARK 3 AUTHORS : DE VLIEG ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS THEN REFINED REMARK 3 AGAINST PRIMARY NOE DATA. THE R VALUE IS 0.19 OVER ALL REMARK 3 OBSERVED, QUANTIFIED, NOE CROSSPEAK INTENSITIES. THE NOE-BASED REMARK 3 PROCEDURE USED TO REFINE THESE STRUCTURES INCLUDED CORRELATION REMARK 3 TIME ADJUSTMENT FACTORS, WHICH ARE APPROXIMATELY RELATED TO REMARK 3 THE INVERSE OF THE TEMPERATURE FACTORS ASSOCIATED WITH X-RAY REMARK 3 CRYSTALLOGRAPHY. THESE VALUES ARE INCLUDED IN THE COLUMN REMARK 3 NORMALLY USED FOR TEMPERATURE FACTORS. VALUES OF 0.0 APPEAR REMARK 3 FOR NON-HYDROGEN ATOMS, WHICH WERE NOT USED IN THE NMR REMARK 3 CALCULATIONS. FURTHER DETAILS ARE GIVEN IN REFERENCE 1. REMARK 4 REMARK 4 1D19 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 : ENERGY MINIMIZATION, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 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 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 DG A 1 C5 DG A 1 N7 -0.062 REMARK 500 DG A 1 N9 DG A 1 C4 -0.050 REMARK 500 DT A 2 C4 DT A 2 C5 -0.057 REMARK 500 DT A 2 C5 DT A 2 C6 0.054 REMARK 500 DT A 2 C5 DT A 2 C7 0.037 REMARK 500 DA A 3 C5 DA A 3 N7 -0.067 REMARK 500 DA A 3 N9 DA A 3 C4 -0.041 REMARK 500 DC A 4 N1 DC A 4 C6 0.038 REMARK 500 DC A 4 C5 DC A 4 C6 0.049 REMARK 500 DG A 5 C5 DG A 5 N7 -0.057 REMARK 500 DT A 6 C5 DT A 6 C6 0.048 REMARK 500 DA A 7 C5 DA A 7 N7 -0.059 REMARK 500 DA A 7 N9 DA A 7 C4 -0.051 REMARK 500 DG B 9 C5 DG B 9 N7 -0.063 REMARK 500 DG B 9 N9 DG B 9 C4 -0.050 REMARK 500 DT B 10 C5 DT B 10 C6 0.042 REMARK 500 DA B 11 C5 DA B 11 N7 -0.059 REMARK 500 DA B 11 N9 DA B 11 C4 -0.041 REMARK 500 DC B 12 C5 DC B 12 C6 0.051 REMARK 500 DG B 13 C5 DG B 13 N7 -0.062 REMARK 500 DG B 13 N9 DG B 13 C4 -0.049 REMARK 500 DT B 14 C5 DT B 14 C6 0.044 REMARK 500 DA B 15 C5 DA B 15 N7 -0.062 REMARK 500 DA B 15 N9 DA B 15 C4 -0.047 REMARK 500 DC B 16 N1 DC B 16 C6 0.037 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 DG A 1 C6 - N1 - C2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DG A 1 N1 - C2 - N3 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG A 1 C2 - N3 - C4 ANGL. DEV. = 9.1 DEGREES REMARK 500 DG A 1 N3 - C4 - C5 ANGL. DEV. = -7.1 DEGREES REMARK 500 DG A 1 C5 - C6 - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 DG A 1 C4 - C5 - N7 ANGL. DEV. = -3.0 DEGREES REMARK 500 DG A 1 N7 - C8 - N9 ANGL. DEV. = -3.3 DEGREES REMARK 500 DG A 1 N3 - C4 - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG A 1 C5 - C6 - O6 ANGL. DEV. = -7.8 DEGREES REMARK 500 DT A 2 N1 - C2 - N3 ANGL. DEV. = 5.3 DEGREES REMARK 500 DT A 2 C2 - N3 - C4 ANGL. DEV. = -5.9 DEGREES REMARK 500 DT A 2 N3 - C4 - C5 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT A 2 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 DA A 3 N1 - C2 - N3 ANGL. DEV. = -6.9 DEGREES REMARK 500 DA A 3 C2 - N3 - C4 ANGL. DEV. = 9.0 DEGREES REMARK 500 DA A 3 N3 - C4 - C5 ANGL. DEV. = -6.9 DEGREES REMARK 500 DA A 3 C5 - N7 - C8 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA A 3 N7 - C8 - N9 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA A 3 N3 - C4 - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 DG A 5 C6 - N1 - C2 ANGL. DEV. = -5.5 DEGREES REMARK 500 DG A 5 C2 - N3 - C4 ANGL. DEV. = 8.4 DEGREES REMARK 500 DG A 5 N3 - C4 - C5 ANGL. DEV. = -7.3 DEGREES REMARK 500 DG A 5 C5 - C6 - N1 ANGL. DEV. = 7.6 DEGREES REMARK 500 DG A 5 C4 - C5 - N7 ANGL. DEV. = -3.4 DEGREES REMARK 500 DG A 5 C5 - N7 - C8 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG A 5 N7 - C8 - N9 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG A 5 N3 - C4 - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 DG A 5 C5 - C6 - O6 ANGL. DEV. = -8.3 DEGREES REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT A 6 N1 - C2 - N3 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT A 6 C2 - N3 - C4 ANGL. DEV. = -6.3 DEGREES REMARK 500 DT A 6 N3 - C4 - C5 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT A 6 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 DA A 7 N1 - C2 - N3 ANGL. DEV. = -6.7 DEGREES REMARK 500 DA A 7 C2 - N3 - C4 ANGL. DEV. = 8.7 DEGREES REMARK 500 DA A 7 N3 - C4 - C5 ANGL. DEV. = -7.0 DEGREES REMARK 500 DA A 7 C5 - N7 - C8 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 7 N7 - C8 - N9 ANGL. DEV. = -3.5 DEGREES REMARK 500 DA A 7 N3 - C4 - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 DG B 9 C6 - N1 - C2 ANGL. DEV. = -5.6 DEGREES REMARK 500 DG B 9 N1 - C2 - N3 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG B 9 C2 - N3 - C4 ANGL. DEV. = 9.6 DEGREES REMARK 500 DG B 9 N3 - C4 - C5 ANGL. DEV. = -8.2 DEGREES REMARK 500 DG B 9 C5 - C6 - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 DG B 9 C4 - C5 - N7 ANGL. DEV. = -3.5 DEGREES REMARK 500 DG B 9 C5 - N7 - C8 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 9 N3 - C4 - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 DG B 9 C5 - C6 - O6 ANGL. DEV. = -7.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 80 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 DG A 1 0.08 SIDE_CHAIN REMARK 500 DT A 2 0.09 SIDE_CHAIN REMARK 500 DA A 3 0.05 SIDE_CHAIN REMARK 500 DC A 4 0.08 SIDE_CHAIN REMARK 500 DG A 5 0.10 SIDE_CHAIN REMARK 500 DT A 6 0.10 SIDE_CHAIN REMARK 500 DG B 9 0.09 SIDE_CHAIN REMARK 500 DT B 10 0.11 SIDE_CHAIN REMARK 500 DC B 12 0.08 SIDE_CHAIN REMARK 500 DG B 13 0.10 SIDE_CHAIN REMARK 500 DT B 14 0.09 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D18 RELATED DB: PDB DBREF 1D19 A 1 8 PDB 1D19 1D19 1 8 DBREF 1D19 B 9 16 PDB 1D19 1D19 9 16 SEQRES 1 A 8 DG DT DA DC DG DT DA DC SEQRES 1 B 8 DG DT DA DC DG DT DA 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 MASTER 202 0 0 0 0 0 0 6 0 0 0 2 END