HEADER DNA 11-JUN-16 5B81 TITLE SOLUTION NMR STRUCTURE OF A 16-MER DNA DUPLEX CONTAINING QUADRUPLE GC TITLE 2 MISMATCHES SHOWING STAGGERED BASE PAIRING, AND CONSEQUENT RESCUE OF TITLE 3 CANONICAL DOUBLE HELICAL CHARACTERISTICS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*GP*CP*AP*TP*GP*CP*GP*CP*TP*AP*CP*GP*CP*G)- COMPND 3 3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*TP*AP*CP*GP*CP*GP*AP*TP*GP*CP*GP*C)- COMPND 9 3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS MISMATCH, MUTS ALPHA, B-DNA, WATSON-CRICK BASE PAIRING, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.DE,S.CHATTERJEE REVDAT 2 01-MAY-24 5B81 1 COMPND REMARK REVDAT 1 29-JUN-16 5B81 0 JRNL AUTH M.DE,S.CHATTERJEE JRNL TITL SOLUTION NMR STRUCTURE OF A 16-MER DNA DUPLEX CONTAINING JRNL TITL 2 QUADRUPLE GC MISMATCHES SHOWING STAGGERED BASE PAIRING, AND JRNL TITL 3 CONSEQUENT RESCUE OF CANONICAL DOUBLE HELICAL JRNL TITL 4 CHARACTERISTICS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 14 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5B81 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1300000687. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 288 REMARK 210 PH : 7.2; 7.2 REMARK 210 IONIC STRENGTH : 50, SODIUM, CHLORIDE; 50, REMARK 210 SODIUM, CHLORIDE REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 350 UM UNLABELLED MISMATCHED REMARK 210 DNA, 95% H2O/5% D2O; 350 UM REMARK 210 UNLABELLED MISMATCH DNA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER 14, SPARKY 3.114 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: 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: 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 C8 DG A 1 N9 0.061 REMARK 500 1 DG A 1 C2 DG A 1 N2 -0.078 REMARK 500 1 DG A 3 C5' DG A 3 C4' 0.057 REMARK 500 1 DG A 3 O4' DG A 3 C4' -0.085 REMARK 500 1 DG A 3 N3 DG A 3 C4 0.062 REMARK 500 1 DG A 3 N9 DG A 3 C4 -0.049 REMARK 500 1 DC A 4 C2' DC A 4 C1' -0.084 REMARK 500 1 DA A 5 N3 DA A 5 C4 0.063 REMARK 500 1 DT A 6 P DT A 6 O5' -0.073 REMARK 500 1 DG A 7 C5' DG A 7 C4' 0.046 REMARK 500 1 DG A 7 N1 DG A 7 C2 -0.056 REMARK 500 1 DG A 7 N7 DG A 7 C8 0.053 REMARK 500 1 DG A 7 C8 DG A 7 N9 -0.047 REMARK 500 1 DC A 8 C4 DC A 8 N4 -0.054 REMARK 500 1 DC A 8 N3 DC A 8 C4 -0.048 REMARK 500 1 DG A 9 C5' DG A 9 C4' 0.058 REMARK 500 1 DG A 9 O4' DG A 9 C4' -0.073 REMARK 500 1 DC A 10 C4 DC A 10 N4 -0.068 REMARK 500 1 DT A 11 C5' DT A 11 C4' 0.059 REMARK 500 1 DT A 11 O4' DT A 11 C4' -0.062 REMARK 500 1 DT A 11 O3' DT A 11 C3' -0.038 REMARK 500 1 DT A 11 C5 DT A 11 C6 0.055 REMARK 500 1 DT A 11 O3' DA A 12 P -0.093 REMARK 500 1 DA A 12 N3 DA A 12 C4 0.041 REMARK 500 1 DA A 12 C5 DA A 12 N7 -0.067 REMARK 500 1 DA A 12 N9 DA A 12 C4 0.064 REMARK 500 1 DC A 13 C5' DC A 13 C4' 0.042 REMARK 500 1 DC A 13 N1 DC A 13 C6 -0.050 REMARK 500 1 DG A 14 O4' DG A 14 C4' -0.060 REMARK 500 1 DG A 14 C2 DG A 14 N3 -0.067 REMARK 500 1 DG A 14 C6 DG A 14 N1 0.050 REMARK 500 1 DG A 14 C5 DG A 14 N7 0.054 REMARK 500 1 DG A 14 C2 DG A 14 N2 -0.087 REMARK 500 1 DC A 15 C2 DC A 15 N3 0.077 REMARK 500 1 DG A 16 P DG A 16 O5' 0.072 REMARK 500 1 DG A 16 O3' DG A 16 C3' -0.088 REMARK 500 1 DG A 16 C4 DG A 16 C5 0.050 REMARK 500 1 DG B 18 C5' DG B 18 C4' 0.094 REMARK 500 1 DG B 18 C2' DG B 18 C1' -0.070 REMARK 500 1 DC B 19 C5' DC B 19 C4' 0.075 REMARK 500 1 DT B 21 O4' DT B 21 C4' -0.074 REMARK 500 1 DT B 21 C5 DT B 21 C7 0.050 REMARK 500 1 DA B 22 C2 DA B 22 N3 -0.056 REMARK 500 1 DC B 23 N3 DC B 23 C4 -0.046 REMARK 500 1 DG B 24 C5' DG B 24 C4' 0.044 REMARK 500 1 DG B 24 C4' DG B 24 C3' 0.066 REMARK 500 1 DG B 24 N3 DG B 24 C4 0.053 REMARK 500 1 DG B 24 C6 DG B 24 N1 -0.061 REMARK 500 1 DC B 25 P DC B 25 O5' 0.061 REMARK 500 1 DC B 25 C5' DC B 25 C4' 0.043 REMARK 500 REMARK 500 THIS ENTRY HAS 1312 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 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DG A 1 O4' - C1' - C2' ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG A 1 C8 - N9 - C4 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG A 1 N1 - C2 - N2 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DC A 2 C2 - N3 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DC A 2 N3 - C4 - C5 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DC A 2 N3 - C4 - N4 ANGL. DEV. = -8.0 DEGREES REMARK 500 1 DG A 3 O4' - C4' - C3' ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DG A 3 N3 - C2 - N2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DA A 5 C6 - N1 - C2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DA A 5 N1 - C2 - N3 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 5 C4 - C5 - C6 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DA A 5 C5 - C6 - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DA A 5 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA A 5 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DT A 6 O4' - C4' - C3' ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DT A 6 C4' - C3' - C2' ANGL. DEV. = -6.9 DEGREES REMARK 500 1 DT A 6 C6 - N1 - C2 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DT A 6 C2 - N3 - C4 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT A 6 C5 - C6 - N1 ANGL. DEV. = -6.7 DEGREES REMARK 500 1 DT A 6 N3 - C4 - O4 ANGL. DEV. = -10.0 DEGREES REMARK 500 1 DT A 6 C5 - C4 - O4 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DG A 7 C1' - O4' - C4' ANGL. DEV. = -10.9 DEGREES REMARK 500 1 DG A 7 N1 - C6 - O6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 7 C5 - C6 - O6 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC A 8 C6 - N1 - C2 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DC A 8 N3 - C4 - C5 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC A 8 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DC A 8 N1 - C2 - O2 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DC A 8 N3 - C2 - O2 ANGL. DEV. = -7.8 DEGREES REMARK 500 1 DC A 8 N3 - C4 - N4 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG A 9 N1 - C2 - N3 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG A 9 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG A 9 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 9 C4 - C5 - N7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 9 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DG A 9 N9 - C4 - C5 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DG A 9 N3 - C4 - N9 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 9 C6 - C5 - N7 ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DG A 9 N3 - C2 - N2 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DG A 9 N1 - C6 - O6 ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DC A 10 C5' - C4' - O4' ANGL. DEV. = 12.2 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 3279 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 1 DT A 6 0.07 SIDE CHAIN REMARK 500 1 DG A 7 0.15 SIDE CHAIN REMARK 500 1 DC A 8 0.17 SIDE CHAIN REMARK 500 1 DT A 11 0.11 SIDE CHAIN REMARK 500 1 DC A 13 0.09 SIDE CHAIN REMARK 500 1 DC A 15 0.07 SIDE CHAIN REMARK 500 1 DG A 16 0.10 SIDE CHAIN REMARK 500 1 DC B 17 0.08 SIDE CHAIN REMARK 500 1 DG B 18 0.09 SIDE CHAIN REMARK 500 1 DT B 21 0.11 SIDE CHAIN REMARK 500 1 DA B 22 0.10 SIDE CHAIN REMARK 500 1 DG B 24 0.10 SIDE CHAIN REMARK 500 1 DC B 25 0.07 SIDE CHAIN REMARK 500 1 DG B 26 0.07 SIDE CHAIN REMARK 500 1 DA B 27 0.16 SIDE CHAIN REMARK 500 1 DG B 29 0.10 SIDE CHAIN REMARK 500 1 DG B 31 0.07 SIDE CHAIN REMARK 500 2 DG A 1 0.08 SIDE CHAIN REMARK 500 2 DC A 2 0.14 SIDE CHAIN REMARK 500 2 DC A 4 0.11 SIDE CHAIN REMARK 500 2 DA A 5 0.07 SIDE CHAIN REMARK 500 2 DT A 6 0.11 SIDE CHAIN REMARK 500 2 DG A 7 0.15 SIDE CHAIN REMARK 500 2 DC A 8 0.16 SIDE CHAIN REMARK 500 2 DG A 9 0.09 SIDE CHAIN REMARK 500 2 DC A 10 0.09 SIDE CHAIN REMARK 500 2 DT A 11 0.14 SIDE CHAIN REMARK 500 2 DA A 12 0.07 SIDE CHAIN REMARK 500 2 DC A 13 0.07 SIDE CHAIN REMARK 500 2 DC A 15 0.07 SIDE CHAIN REMARK 500 2 DC B 17 0.13 SIDE CHAIN REMARK 500 2 DG B 18 0.13 SIDE CHAIN REMARK 500 2 DC B 19 0.08 SIDE CHAIN REMARK 500 2 DT B 21 0.10 SIDE CHAIN REMARK 500 2 DG B 26 0.10 SIDE CHAIN REMARK 500 2 DA B 27 0.09 SIDE CHAIN REMARK 500 2 DT B 28 0.08 SIDE CHAIN REMARK 500 2 DC B 30 0.09 SIDE CHAIN REMARK 500 2 DG B 31 0.09 SIDE CHAIN REMARK 500 2 DC B 32 0.10 SIDE CHAIN REMARK 500 3 DG A 1 0.07 SIDE CHAIN REMARK 500 3 DT A 6 0.15 SIDE CHAIN REMARK 500 3 DG A 7 0.12 SIDE CHAIN REMARK 500 3 DC A 8 0.19 SIDE CHAIN REMARK 500 3 DG A 9 0.06 SIDE CHAIN REMARK 500 3 DC A 10 0.09 SIDE CHAIN REMARK 500 3 DT A 11 0.09 SIDE CHAIN REMARK 500 3 DC A 13 0.13 SIDE CHAIN REMARK 500 3 DG A 14 0.07 SIDE CHAIN REMARK 500 3 DG A 16 0.10 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 385 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36003 RELATED DB: BMRB DBREF 5B81 A 1 16 PDB 5B81 5B81 1 16 DBREF 5B81 B 17 32 PDB 5B81 5B81 17 32 SEQRES 1 A 16 DG DC DG DC DA DT DG DC DG DC DT DA DC SEQRES 2 A 16 DG DC DG SEQRES 1 B 16 DC DG DC DG DT DA DC DG DC DG DA DT DG SEQRES 2 B 16 DC DG 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