HEADER DNA 23-JUL-15 2N5P TITLE UNIVERSAL BASE CONTROL OLIGONUCLEOTIDE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA_(5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA_(5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'); COMPND 7 CHAIN: B; COMPND 8 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 NUCLEIC ACID, DNA, UNIVERSAL BASE, SYNTHETIC BASE EXPDTA SOLUTION NMR AUTHOR A.M.SPRING-CONNELL,M.G.EVICH,F.SEELA,M.W.GERMANN REVDAT 3 01-MAY-24 2N5P 1 REMARK REVDAT 2 28-DEC-16 2N5P 1 JRNL REVDAT 1 07-SEP-16 2N5P 0 JRNL AUTH A.M.SPRING-CONNELL,M.G.EVICH,H.DEBELAK,F.SEELA,M.W.GERMANN JRNL TITL USING NMR AND MOLECULAR DYNAMICS TO LINK STRUCTURE AND JRNL TITL 2 DYNAMICS EFFECTS OF THE UNIVERSAL BASE 8-AZA, 7-DEAZA, N8 JRNL TITL 3 LINKED ADENOSINE ANALOG. JRNL REF NUCLEIC ACIDS RES. V. 44 8576 2016 JRNL REFN ISSN 0305-1048 JRNL PMID 27566150 JRNL DOI 10.1093/NAR/GKW736 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9, AMBER 9, CORMA, MARDIGRAS REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN (AMBER), CASE, DARDEN, REMARK 3 CHEATHAM, III, SIMMERLING, WANG, DUKE, LUO, ... REMARK 3 AND KOLLMAN (AMBER), THOMAS JAMES (CORMA), THOMAS REMARK 3 JAMES (MARDIGRAS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AMBER 9 RESTRAINED MD SIMULATIONS, REMARK 3 MARDIGRAS, CORMA FOR COMPARISONS OF STRUCTURE TO NOE DATA (RX REMARK 3 VALUES). REMARK 4 REMARK 4 2N5P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000104454. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 294 REMARK 210 PH : 6.79 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM DNA (5' REMARK 210 -D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3'), 1 MM DNA (5'-D(*GP*AP*GP*CP* REMARK 210 TP*CP*CP*AP*T)-3'), 100 % 100% DEUTERIUM D2O, 100 MM SODIUM REMARK 210 CHLORIDE, 10 MM SODIUM PHOSPHATE, 100% D2O; 1 MM DNA (5'-D(*AP* REMARK 210 TP*GP*GP*AP*GP*CP*TP*C)-3'), 1 MM DNA (5'-D(*GP*AP*GP*CP*TP*CP* REMARK 210 CP*AP*T)-3'), 100 MM SODIUM CHLORIDE, 10 MM SODIUM PHOSPHATE, 90 REMARK 210 % H2O, 10 % 100% DEUTERIUM D2O, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY 75 MS; 2D LOW REMARK 210 FLIP COSY; 2D 1H-13C HSQC; 2D 1H- REMARK 210 1H CONSTANT TIME NOESY; 2D 1H-1H REMARK 210 TOCSY; 2D 1H-31P CORR; 1D 1H; 1D REMARK 210 1H 1-1 JUMP AND RETURN; 1D 31P; REMARK 210 2D 1H-1H NOESY 150 MS; 2D 1H-1H REMARK 210 NOESY 250 MS REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, XWINNMR, CORMA, REMARK 210 MARDIGRAS REMARK 210 METHOD USED : MOLECULAR DYNAMICS, MATRIX REMARK 210 RELAXATION, DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM 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 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 1 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 1 C4 - C5 - C6 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA A 1 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG A 4 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES REMARK 500 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 DA A 5 C5 - C6 - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA A 5 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC A 7 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 7 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC A 9 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA B 11 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 DA B 11 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA B 11 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG B 12 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT B 14 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DC B 16 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA B 17 O4' - C4' - C3' ANGL. DEV. = 5.7 DEGREES REMARK 500 DA B 17 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA B 17 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA B 17 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 DT B 18 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES 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 4 0.07 SIDE CHAIN REMARK 500 DT A 8 0.06 SIDE CHAIN REMARK 500 DC A 9 0.07 SIDE CHAIN REMARK 500 DT B 18 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25724 RELATED DB: BMRB REMARK 900 RELATED ID: 2N5O RELATED DB: PDB DBREF 2N5P A 1 9 PDB 2N5P 2N5P 1 9 DBREF 2N5P B 10 18 PDB 2N5P 2N5P 10 18 SEQRES 1 A 9 DA DT DG DG DA DG DC DT DC SEQRES 1 B 9 DG DA DG DC DT DC DC 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