10 20 30 40 50 60 70 80 1D18 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 01-AUG-90 1D18
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(*CP*AP*TP*GP*CP*AP*TP*G)-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 5 24-FEB-09 1D18 1 VERSN REVDAT 4 01-APR-03 1D18 1 JRNL REVDAT 3 15-OCT-94 1D18 1 COMPND EXPDTA REVDAT 2 15-JAN-93 1D18 1 HEADER REVDAT 1 15-JUL-91 1D18 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 REFINED AGAINST REMARK 3 PRIMARY NOE DATA. THE R VALUE IS 0.23 OVER ALL OBSERVED, REMARK 3 QUANTIFIED, NOE CROSSPEAK INTENSITIES. THE NOE-BASED PROCEDURE REMARK 3 USED TO REFINE THESE STRUCTURES INCLUDED CORRELATION TIME REMARK 3 ADJUSTMENT FACTORS, WHICH ARE APPROXIMATELY RELATED TO THE REMARK 3 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 1D18 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 DC A 1 N1 DC A 1 C6 0.040 REMARK 500 DA A 2 C5 DA A 2 N7 -0.069 REMARK 500 DA A 2 N9 DA A 2 C4 -0.042 REMARK 500 DT A 3 C5 DT A 3 C6 0.043 REMARK 500 DG A 4 C5 DG A 4 N7 -0.062 REMARK 500 DC A 5 N1 DC A 5 C6 0.038 REMARK 500 DA A 6 C5 DA A 6 N7 -0.063 REMARK 500 DA A 6 N9 DA A 6 C4 -0.048 REMARK 500 DT A 7 C4 DT A 7 C5 -0.057 REMARK 500 DT A 7 C5 DT A 7 C6 0.052 REMARK 500 DG A 8 C5 DG A 8 N7 -0.066 REMARK 500 DG A 8 N9 DG A 8 C4 -0.054 REMARK 500 DC B 9 N1 DC B 9 C6 0.039 REMARK 500 DA B 10 C5 DA B 10 N7 -0.062 REMARK 500 DA B 10 N9 DA B 10 C4 -0.051 REMARK 500 DT B 11 C5 DT B 11 C6 0.047 REMARK 500 DT B 11 C5 DT B 11 C7 0.036 REMARK 500 DG B 12 C5 DG B 12 N7 -0.063 REMARK 500 DG B 12 C8 DG B 12 N9 -0.045 REMARK 500 DA B 14 C5 DA B 14 N7 -0.059 REMARK 500 DA B 14 N9 DA B 14 C4 -0.044 REMARK 500 DT B 15 C4 DT B 15 C5 -0.060 REMARK 500 DT B 15 C5 DT B 15 C6 0.053 REMARK 500 DG B 16 C5 DG B 16 N7 -0.056 REMARK 500 DG B 16 N9 DG B 16 C4 -0.053 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 DA A 2 N1 - C2 - N3 ANGL. DEV. = -7.0 DEGREES REMARK 500 DA A 2 C2 - N3 - C4 ANGL. DEV. = 8.8 DEGREES REMARK 500 DA A 2 N3 - C4 - C5 ANGL. DEV. = -6.6 DEGREES REMARK 500 DA A 2 C5 - N7 - C8 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 2 N7 - C8 - N9 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA A 2 N3 - C4 - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 DT A 3 N1 - C2 - N3 ANGL. DEV. = 5.1 DEGREES REMARK 500 DT A 3 C2 - N3 - C4 ANGL. DEV. = -5.8 DEGREES REMARK 500 DT A 3 N3 - C4 - C5 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT A 3 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG A 4 C6 - N1 - C2 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG A 4 N1 - C2 - N3 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG A 4 C2 - N3 - C4 ANGL. DEV. = 9.0 DEGREES REMARK 500 DG A 4 N3 - C4 - C5 ANGL. DEV. = -7.2 DEGREES REMARK 500 DG A 4 C5 - C6 - N1 ANGL. DEV. = 6.5 DEGREES REMARK 500 DG A 4 C4 - C5 - N7 ANGL. DEV. = -2.5 DEGREES REMARK 500 DG A 4 N3 - C4 - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 DG A 4 C5 - C6 - O6 ANGL. DEV. = -8.2 DEGREES REMARK 500 DC A 5 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 6 N1 - C2 - N3 ANGL. DEV. = -6.6 DEGREES REMARK 500 DA A 6 C2 - N3 - C4 ANGL. DEV. = 9.3 DEGREES REMARK 500 DA A 6 N3 - C4 - C5 ANGL. DEV. = -7.6 DEGREES REMARK 500 DA A 6 C4 - C5 - N7 ANGL. DEV. = -3.0 DEGREES REMARK 500 DA A 6 C5 - N7 - C8 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 6 N7 - C8 - N9 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA A 6 N3 - C4 - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 DT A 7 C1' - O4' - C4' ANGL. DEV. = -6.7 DEGREES REMARK 500 DT A 7 N1 - C2 - N3 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT A 7 C2 - N3 - C4 ANGL. DEV. = -6.0 DEGREES REMARK 500 DT A 7 N3 - C4 - C5 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT A 7 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DT A 7 C6 - C5 - C7 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG A 8 C6 - N1 - C2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG A 8 N1 - C2 - N3 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG A 8 C2 - N3 - C4 ANGL. DEV. = 9.1 DEGREES REMARK 500 DG A 8 N3 - C4 - C5 ANGL. DEV. = -7.0 DEGREES REMARK 500 DG A 8 C5 - C6 - N1 ANGL. DEV. = 6.7 DEGREES REMARK 500 DG A 8 C4 - C5 - N7 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG A 8 N7 - C8 - N9 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG A 8 N3 - C4 - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 DG A 8 C5 - C6 - O6 ANGL. DEV. = -8.1 DEGREES REMARK 500 DA B 10 N1 - C2 - N3 ANGL. DEV. = -6.9 DEGREES REMARK 500 DA B 10 C2 - N3 - C4 ANGL. DEV. = 9.3 DEGREES REMARK 500 DA B 10 N3 - C4 - C5 ANGL. DEV. = -7.3 DEGREES REMARK 500 DA B 10 N7 - C8 - N9 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA B 10 N3 - C4 - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 DT B 11 N1 - C2 - N3 ANGL. DEV. = 4.7 DEGREES REMARK 500 DT B 11 C2 - N3 - C4 ANGL. DEV. = -5.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 83 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 DC A 1 0.07 SIDE_CHAIN REMARK 500 DA A 2 0.08 SIDE_CHAIN REMARK 500 DC A 5 0.10 SIDE_CHAIN REMARK 500 DA A 6 0.14 SIDE_CHAIN REMARK 500 DC B 9 0.09 SIDE_CHAIN REMARK 500 DA B 10 0.06 SIDE_CHAIN REMARK 500 DG B 12 0.07 SIDE_CHAIN REMARK 500 DC B 13 0.09 SIDE_CHAIN REMARK 500 DA B 14 0.12 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D19 RELATED DB: PDB
DBREF 1D18 A 1 8 PDB 1D18 1D18 1 8 DBREF 1D18 B 9 16 PDB 1D18 1D18 9 16
SEQRES 1 A 8 DC DA DT DG DC DA DT DG SEQRES 1 B 8 DC DA DT DG DC DA DT DG
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