HEADER DNA 14-DEC-98 1B3P TITLE 5'-D(*GP*GP*AP*GP*GP*AP*T)-3' COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*AP*GP*GP*AP*T)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS (G-G-A) TRIPLET REPEAT; V-SHAPED BACKBONE; PARALLEL- KEYWDS 2 STRANDED SEGMENTS; MISMATCH ALIGNMENTS; UNIFORM 13C, 15N- KEYWDS 3 LABELED DNA EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR A.KETTANI,S.BOUAZIZ,E.SKRIPKIN,A.MAJUMDAR,W.WANG,R.A.JONES, AUTHOR 2 D.J.PATEL REVDAT 2 24-FEB-09 1B3P 1 VERSN REVDAT 1 31-AUG-99 1B3P 0 JRNL AUTH A.KETTANI,S.BOUAZIZ,E.SKRIPKIN,A.MAJUMDAR,W.WANG, JRNL AUTH 2 R.A.JONES,D.J.PATEL JRNL TITL INTERLOCKED MISMATCH-ALIGNED ARROWHEAD DNA MOTIFS. JRNL REF STRUCTURE FOLD.DES. V. 7 803 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10425682 JRNL DOI 10.1016/S0969-2126(99)80104-X REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN REMARK 3 THE JNRL CITATION ABOVE REMARK 4 REMARK 4 1B3P COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-98. REMARK 100 THE RCSB ID CODE IS RCSB000272. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 273 REMARK 210 PH : 6.6 REMARK 210 IONIC STRENGTH : 10 MM NACL, 2 MM PHOSPHATE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, COSY, TOCSY, 13C- REMARK 210 EDITED 13C-PURGED NOESY, 15N- REMARK 210 EDITED 15N-PURGED NOESY, HNN- REMARK 210 COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.851 REMARK 210 METHOD USED : DISTANCE-GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : ACCEPTABLE COVALENT GEOMETRY, REMARK 210 LOW DISTANCE RESTRAINTS REMARK 210 VIIOLATIONS AND FAVORABLE NON- REMARK 210 BONDED ENERGY VALUES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR AND REMARK 210 HETERONUCLEAR EXPERIMENTS ON 13C AND 15N LABELED SAMPLE. THE REMARK 210 DISTANCE RESTRAINTS WERE DEDUCED FROM 5 NOESY MIXING TIMES REMARK 210 (50, 100, 150, 200 AND 250 MS) IN D2O AND 2 NOESY MIXING TIMES REMARK 210 IN H2O (60 AND 200 MS) MS 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 1 DG A 1 C5' DG A 1 C4' 0.063 REMARK 500 1 DG A 2 C5' DG A 2 C4' 0.088 REMARK 500 1 DA A 3 C5' DA A 3 C4' 0.062 REMARK 500 1 DG A 5 C5' DG A 5 C4' 0.059 REMARK 500 1 DA A 6 C5' DA A 6 C4' 0.054 REMARK 500 1 DG B 1 C5' DG B 1 C4' 0.063 REMARK 500 1 DG B 2 C5' DG B 2 C4' 0.088 REMARK 500 1 DA B 3 C5' DA B 3 C4' 0.063 REMARK 500 1 DG B 5 C5' DG B 5 C4' 0.060 REMARK 500 1 DA B 6 C5' DA B 6 C4' 0.054 REMARK 500 2 DG A 1 C5' DG A 1 C4' 0.081 REMARK 500 2 DG A 2 C5' DG A 2 C4' 0.089 REMARK 500 2 DA A 3 C5' DA A 3 C4' 0.074 REMARK 500 2 DG A 5 C5' DG A 5 C4' 0.065 REMARK 500 2 DA A 6 C5' DA A 6 C4' 0.063 REMARK 500 2 DG B 1 C5' DG B 1 C4' 0.080 REMARK 500 2 DG B 2 C5' DG B 2 C4' 0.089 REMARK 500 2 DA B 3 C5' DA B 3 C4' 0.073 REMARK 500 2 DG B 5 C5' DG B 5 C4' 0.064 REMARK 500 2 DA B 6 C5' DA B 6 C4' 0.064 REMARK 500 3 DG A 1 C5' DG A 1 C4' 0.077 REMARK 500 3 DG A 2 C5' DG A 2 C4' 0.089 REMARK 500 3 DA A 3 C5' DA A 3 C4' 0.076 REMARK 500 3 DG A 5 C5' DG A 5 C4' 0.059 REMARK 500 3 DA A 6 C5' DA A 6 C4' 0.046 REMARK 500 3 DT A 7 C5 DT A 7 C7 0.039 REMARK 500 3 DG B 1 C5' DG B 1 C4' 0.076 REMARK 500 3 DG B 2 C5' DG B 2 C4' 0.090 REMARK 500 3 DA B 3 C5' DA B 3 C4' 0.076 REMARK 500 3 DG B 5 C5' DG B 5 C4' 0.061 REMARK 500 3 DA B 6 C5' DA B 6 C4' 0.042 REMARK 500 3 DT B 7 C5' DT B 7 C4' 0.055 REMARK 500 4 DG A 1 C5' DG A 1 C4' 0.073 REMARK 500 4 DG A 2 C5' DG A 2 C4' 0.088 REMARK 500 4 DA A 3 C5' DA A 3 C4' 0.064 REMARK 500 4 DG A 4 C5' DG A 4 C4' 0.062 REMARK 500 4 DG A 5 C5' DG A 5 C4' 0.054 REMARK 500 4 DT A 7 C5 DT A 7 C7 0.042 REMARK 500 4 DG B 1 C5' DG B 1 C4' 0.073 REMARK 500 4 DG B 2 C5' DG B 2 C4' 0.085 REMARK 500 4 DA B 3 C5' DA B 3 C4' 0.063 REMARK 500 4 DG B 4 C5' DG B 4 C4' 0.060 REMARK 500 4 DG B 5 C5' DG B 5 C4' 0.055 REMARK 500 4 DT B 7 C5 DT B 7 C7 0.042 REMARK 500 5 DG A 1 C5' DG A 1 C4' 0.078 REMARK 500 5 DG A 2 C5' DG A 2 C4' 0.088 REMARK 500 5 DA A 3 C5' DA A 3 C4' 0.073 REMARK 500 5 DG A 5 C5' DG A 5 C4' 0.053 REMARK 500 5 DA A 6 C5' DA A 6 C4' 0.055 REMARK 500 5 DT A 7 C5 DT A 7 C7 0.041 REMARK 500 REMARK 500 THIS ENTRY HAS 163 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 1 C5' - C4' - C3' ANGL. DEV. = 11.3 DEGREES REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG A 2 C4' - C3' - O3' ANGL. DEV. = 12.2 DEGREES REMARK 500 1 DG A 2 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG A 2 O4' - C1' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 4 O4' - C1' - C2' ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DG A 5 O4' - C1' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DA A 6 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DA A 6 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DG B 1 C5' - C4' - C3' ANGL. DEV. = 11.4 DEGREES REMARK 500 1 DG B 1 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 2 C4' - C3' - O3' ANGL. DEV. = 12.4 DEGREES REMARK 500 1 DG B 2 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG B 2 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 1 DG B 2 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG B 4 O4' - C1' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DG B 5 O4' - C1' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DG B 5 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DA B 6 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DA B 6 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DT B 7 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DA B 6 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DG A 2 C4' - C3' - O3' ANGL. DEV. = 12.2 DEGREES REMARK 500 2 DG A 2 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DG A 2 O4' - C1' - C2' ANGL. DEV. = -7.9 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 8.6 DEGREES REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DG A 4 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DG A 4 O4' - C1' - C2' ANGL. DEV. = -7.4 DEGREES REMARK 500 2 DG A 5 O4' - C1' - C2' ANGL. DEV. = -8.1 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 DA A 6 O4' - C4' - C3' ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DG A 5 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES REMARK 500 2 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DG B 1 O4' - C1' - N9 ANGL. DEV. = -5.9 DEGREES REMARK 500 2 DG B 2 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DG B 2 O4' - C1' - C2' ANGL. DEV. = -7.9 DEGREES REMARK 500 2 DG B 2 O4' - C1' - N9 ANGL. DEV. = 8.6 DEGREES REMARK 500 2 DA B 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG B 4 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DG B 4 O4' - C1' - C2' ANGL. DEV. = -7.4 DEGREES REMARK 500 2 DG B 5 O4' - C1' - C2' ANGL. DEV. = -8.1 DEGREES REMARK 500 2 DG B 5 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 416 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1B3P A 1 7 PDB 1B3P 1B3P 1 7 DBREF 1B3P B 1 7 PDB 1B3P 1B3P 1 7 SEQRES 1 A 7 DG DG DA DG DG DA DT SEQRES 1 B 7 DG DG DA DG DG DA 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 ENDMDL MASTER 196 0 0 0 0 0 0 6 0 0 0 2 END