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-STRANDED KEYWDS 2 SEGMENTS; MISMATCH ALIGNMENTS; UNIFORM 13C, 15N-LABELED DNA, DNA EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR A.KETTANI,S.BOUAZIZ,E.SKRIPKIN,A.MAJUMDAR,W.WANG,R.A.JONES,D.J.PATEL REVDAT 4 27-DEC-23 1B3P 1 REMARK REVDAT 3 16-FEB-22 1B3P 1 REMARK 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,R.A.JONES, JRNL AUTH 2 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 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 THE REMARK 3 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 DEPOSITION ID IS D_1000000272. 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-EDITED REMARK 210 13C-PURGED NOESY; 15N-EDITED 15N- REMARK 210 PURGED NOESY; HNN-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 (50, REMARK 210 100, 150, 200 AND 250 MS) IN D2O AND 2 NOESY MIXING TIMES IN H2O REMARK 210 (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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 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. = -4.8 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 DA A 6 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DG B 1 C5' - C4' - C3' ANGL. DEV. = 11.3 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. = 6.0 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 DA B 6 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DT B 7 C6 - C5 - C7 ANGL. DEV. = -4.4 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. = 4.8 DEGREES REMARK 500 2 DG A 5 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 DG A 5 C3' - O3' - P ANGL. DEV. = 8.9 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 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 MODEL 1