HEADER DNA 10-NOV-18 6I4O TITLE DODECAMER DNA CONTAINING THE SYNTHETIC BASE PAIR P-Z COMPND MOL_ID: 1; COMPND 2 MOLECULE: (DCZ)(DG)(DA)(DT)(DP)(DT)(DA)(DZ)(DA)(DT)(DC)(DG3); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DCZ)GAT(.DP)TA(.DZ)ATCG SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DNA, SYNTHETIC BASE PAIR, Z, P EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR G.PADRONI,L.F.REICHENBACH,J.A.PARKINSON,G.A.BURLEY REVDAT 4 03-JUL-24 6I4O 1 REMARK REVDAT 3 03-JUL-24 6I4O 1 REMARK REVDAT 2 10-JUL-19 6I4O 1 JRNL REVDAT 1 12-JUN-19 6I4O 0 JRNL AUTH G.PADRONI,J.M.WITHERS,A.TALADRIZ-SENDER,L.F.REICHENBACH, JRNL AUTH 2 J.A.PARKINSON,G.A.BURLEY JRNL TITL SEQUENCE-SELECTIVE MINOR GROOVE RECOGNITION OF A DNA DUPLEX JRNL TITL 2 CONTAINING SYNTHETIC GENETIC COMPONENTS. JRNL REF J.AM.CHEM.SOC. V. 141 9555 2019 JRNL REFN ESSN 1520-5126 JRNL PMID 31117639 JRNL DOI 10.1021/JACS.8B12444 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, MARDIGRAS, AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN (AMBER), BRANDAN A. REMARK 3 BORGIAS PAUL D. THOMAS HE LIU ANIL KUMAR REMARK 3 (MARDIGRAS), CASE, DARDEN, CHEATHAM III, REMARK 3 SIMMERLING, WANG, DUKE, LUO, ... AND KOLLMAN REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6I4O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1200011932. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 7.5; 7.5 REMARK 210 IONIC STRENGTH : 100; 100 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.3 MM ZP-DNA, 100% D2O; 1.3 MM REMARK 210 ZP-DNA, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D DQF-COSY; 2D REMARK 210 1H-1H TOCSY; 2D 1H-13C HSQC; 2D REMARK 210 31P-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, TOPSPIN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 5000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : CLUSTERING OF MD 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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 1 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DC A 1 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA A 7 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA A 7 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 7 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA A 9 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 9 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC B 13 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DC B 13 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DC B 13 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC B 13 N3 - C2 - O2 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA B 15 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DT B 16 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT B 16 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DA B 19 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA B 19 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA B 19 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA B 21 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA B 21 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA B 21 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT B 22 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT B 22 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC B 23 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DC A 1 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.9 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA A 3 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DT A 4 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 389 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 DG A 2 0.07 SIDE CHAIN REMARK 500 1 DA A 3 0.07 SIDE CHAIN REMARK 500 1 DA A 9 0.07 SIDE CHAIN REMARK 500 1 DT A 10 0.09 SIDE CHAIN REMARK 500 1 DA B 15 0.06 SIDE CHAIN REMARK 500 1 DC B 23 0.06 SIDE CHAIN REMARK 500 1 DG B 24 0.09 SIDE CHAIN REMARK 500 2 DA A 3 0.08 SIDE CHAIN REMARK 500 2 DT A 4 0.06 SIDE CHAIN REMARK 500 2 DT A 10 0.08 SIDE CHAIN REMARK 500 2 DC A 11 0.07 SIDE CHAIN REMARK 500 2 DG A 12 0.09 SIDE CHAIN REMARK 500 2 DG B 14 0.05 SIDE CHAIN REMARK 500 2 DC B 23 0.08 SIDE CHAIN REMARK 500 2 DG B 24 0.10 SIDE CHAIN REMARK 500 3 DG A 2 0.05 SIDE CHAIN REMARK 500 3 DA A 3 0.05 SIDE CHAIN REMARK 500 3 DA A 9 0.06 SIDE CHAIN REMARK 500 3 DT A 10 0.07 SIDE CHAIN REMARK 500 3 DC A 11 0.09 SIDE CHAIN REMARK 500 3 DG A 12 0.06 SIDE CHAIN REMARK 500 3 DA B 15 0.07 SIDE CHAIN REMARK 500 3 DT B 18 0.07 SIDE CHAIN REMARK 500 3 DT B 22 0.06 SIDE CHAIN REMARK 500 3 DC B 23 0.09 SIDE CHAIN REMARK 500 3 DG B 24 0.10 SIDE CHAIN REMARK 500 4 DA A 3 0.07 SIDE CHAIN REMARK 500 4 DA A 9 0.07 SIDE CHAIN REMARK 500 4 DC A 11 0.08 SIDE CHAIN REMARK 500 4 DG A 12 0.08 SIDE CHAIN REMARK 500 4 DG B 14 0.06 SIDE CHAIN REMARK 500 4 DA B 15 0.08 SIDE CHAIN REMARK 500 4 DT B 18 0.09 SIDE CHAIN REMARK 500 4 DA B 21 0.06 SIDE CHAIN REMARK 500 4 DC B 23 0.06 SIDE CHAIN REMARK 500 4 DG B 24 0.11 SIDE CHAIN REMARK 500 5 DG A 2 0.06 SIDE CHAIN REMARK 500 5 DA A 3 0.07 SIDE CHAIN REMARK 500 5 DC A 11 0.06 SIDE CHAIN REMARK 500 5 DG A 12 0.07 SIDE CHAIN REMARK 500 5 DG B 14 0.07 SIDE CHAIN REMARK 500 5 DA B 15 0.06 SIDE CHAIN REMARK 500 5 DT B 18 0.09 SIDE CHAIN REMARK 500 5 DG B 24 0.07 SIDE CHAIN REMARK 500 6 DA A 3 0.06 SIDE CHAIN REMARK 500 6 DC A 11 0.09 SIDE CHAIN REMARK 500 6 DG A 12 0.06 SIDE CHAIN REMARK 500 6 DT B 22 0.09 SIDE CHAIN REMARK 500 6 DC B 23 0.07 SIDE CHAIN REMARK 500 6 DG B 24 0.10 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 72 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34328 RELATED DB: BMRB REMARK 900 DODECAMER DNA CONTAINING THE SYNTHETIC BASE PAIR P-Z DBREF 6I4O A 1 12 PDB 6I4O 6I4O 1 12 DBREF 6I4O B 13 24 PDB 6I4O 6I4O 13 24 SEQRES 1 A 12 DC DG DA DT DP DT DA DZ DA DT DC DG SEQRES 1 B 12 DC DG DA DT DP DT DA DZ DA DT DC DG HET DP A 5 33 HET DZ A 8 33 HET DP B 17 33 HET DZ B 20 33 HETNAM DP [(2~{R},3~{S},5~{R})-5-(2-AZANYL-4-OXIDANYLIDENE- HETNAM 2 DP IMIDAZO[1,2-A][1,3,5]TRIAZIN-8-YL)-3-OXIDANYL-OXOLAN- HETNAM 3 DP 2-YL]METHYL DIHYDROGEN PHOSPHATE HETNAM DZ [(2~{R},3~{S},5~{R})-5-(6-AZANYL-5-NITRO-2- HETNAM 2 DZ OXIDANYLIDENE-1~{H}-PYRIDIN-3-YL)-3-OXIDANYL-OXOLAN-2- HETNAM 3 DZ YL]METHYL DIHYDROGEN PHOSPHATE FORMUL 1 DP 2(C10 H14 N5 O7 P) FORMUL 1 DZ 2(C10 H14 N3 O9 P) LINK O3' DT A 4 P DP A 5 1555 1555 1.61 LINK O3' DP A 5 P DT A 6 1555 1555 1.61 LINK O3' DA A 7 P DZ A 8 1555 1555 1.62 LINK O3' DZ A 8 P DA A 9 1555 1555 1.61 LINK O3' DT B 16 P DP B 17 1555 1555 1.61 LINK O3' DP B 17 P DT B 18 1555 1555 1.61 LINK O3' DA B 19 P DZ B 20 1555 1555 1.61 LINK O3' DZ B 20 P DA B 21 1555 1555 1.61 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