HEADER DNA 10-NOV-18 6I4N TITLE DODECAMER DNA CONTAINING THE SYNTHETIC BASE PAIR P-Z IN COMPLEX WITH A TITLE 2 PYRROLE-IMIDAZOLE POLYAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES 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, PYRROLE-IMIDAZOLE POLYAMIDE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR G.PADRONI,J.PARKISON,G.A.BURLEY REVDAT 2 10-JUL-19 6I4N 1 JRNL REVDAT 1 12-JUN-19 6I4N 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, AMBER 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, ... AND REMARK 3 KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6I4N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-APR-19. REMARK 100 THE DEPOSITION ID IS D_1200011958. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.3 MM DNA (5' REMARK 210 -D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3'), 100% D2O; 1.3 REMARK 210 MM DNA (5'-D(*CP*GP*AP*TP*(DP)P*TP*AP*(DZ)P*AP*TP*CP*G)-3'), 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D DQF-COSY; 2D 1H-1H REMARK 210 TOCSY; 2D 1H-13C HSQC; 31P -1H REMARK 210 COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCEII+ REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, MARDIGRAS 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 : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY 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: 1840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 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' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.0 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. = 3.9 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA A 7 C5 - C6 - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DA A 7 N1 - C6 - N6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA A 9 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 9 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC B 13 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC B 13 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.7 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. = 2.0 DEGREES REMARK 500 1 DT B 16 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT B 16 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT B 18 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA B 19 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA B 19 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA B 21 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA B 21 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DT B 22 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT B 22 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT B 22 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC B 23 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DC B 23 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA A 3 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DA A 7 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DA A 7 N1 - C6 - N6 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DA A 9 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA A 9 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 DT A 10 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 2 DT A 10 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DC A 11 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 337 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 DC A 1 0.07 SIDE CHAIN REMARK 500 1 DG A 2 0.06 SIDE CHAIN REMARK 500 1 DT A 6 0.12 SIDE CHAIN REMARK 500 1 DT B 18 0.07 SIDE CHAIN REMARK 500 1 DC B 23 0.06 SIDE CHAIN REMARK 500 1 DG B 24 0.11 SIDE CHAIN REMARK 500 2 DG A 2 0.06 SIDE CHAIN REMARK 500 2 DT A 6 0.09 SIDE CHAIN REMARK 500 2 DT B 18 0.08 SIDE CHAIN REMARK 500 3 DC A 1 0.07 SIDE CHAIN REMARK 500 3 DG A 2 0.07 SIDE CHAIN REMARK 500 3 DT A 6 0.11 SIDE CHAIN REMARK 500 3 DA A 7 0.06 SIDE CHAIN REMARK 500 3 DC B 23 0.07 SIDE CHAIN REMARK 500 3 DG B 24 0.09 SIDE CHAIN REMARK 500 4 DT A 6 0.10 SIDE CHAIN REMARK 500 4 DA A 7 0.05 SIDE CHAIN REMARK 500 4 DT B 18 0.08 SIDE CHAIN REMARK 500 4 DG B 24 0.10 SIDE CHAIN REMARK 500 5 DG A 2 0.06 SIDE CHAIN REMARK 500 5 DT A 6 0.08 SIDE CHAIN REMARK 500 5 DA B 19 0.06 SIDE CHAIN REMARK 500 6 DT A 6 0.10 SIDE CHAIN REMARK 500 6 DT B 18 0.07 SIDE CHAIN REMARK 500 6 DG B 24 0.07 SIDE CHAIN REMARK 500 7 DT A 4 0.07 SIDE CHAIN REMARK 500 7 DT A 6 0.09 SIDE CHAIN REMARK 500 7 DT B 18 0.09 SIDE CHAIN REMARK 500 7 DC B 23 0.09 SIDE CHAIN REMARK 500 8 DT A 6 0.11 SIDE CHAIN REMARK 500 8 DA A 7 0.06 SIDE CHAIN REMARK 500 8 DT B 18 0.08 SIDE CHAIN REMARK 500 8 DA B 19 0.05 SIDE CHAIN REMARK 500 8 DC B 23 0.06 SIDE CHAIN REMARK 500 8 DG B 24 0.08 SIDE CHAIN REMARK 500 9 DT A 6 0.07 SIDE CHAIN REMARK 500 9 DA A 7 0.07 SIDE CHAIN REMARK 500 9 DC B 13 0.06 SIDE CHAIN REMARK 500 9 DA B 15 0.06 SIDE CHAIN REMARK 500 9 DT B 18 0.06 SIDE CHAIN REMARK 500 9 DG B 24 0.07 SIDE CHAIN REMARK 500 10 DG A 2 0.06 SIDE CHAIN REMARK 500 10 DT A 6 0.08 SIDE CHAIN REMARK 500 10 DC A 11 0.08 SIDE CHAIN REMARK 500 10 DG A 12 0.07 SIDE CHAIN REMARK 500 10 DG B 14 0.06 SIDE CHAIN REMARK 500 10 DT B 18 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K4Z B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DT B 16 and DP B REMARK 800 17 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DP B 17 and DT B REMARK 800 18 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DA B 19 and DZ B REMARK 800 20 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DZ B 20 and DA B REMARK 800 21 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34327 RELATED DB: BMRB REMARK 900 DODECAMER DNA CONTAINING THE SYNTHETIC BASE PAIR P-Z IN COMPLEX REMARK 900 WITH A PYRROLE-IMIDAZOLE POLYAMIDE DBREF 6I4N A 1 12 PDB 6I4N 6I4N 1 12 DBREF 6I4N B 13 24 PDB 6I4N 6I4N 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 HET K4Z B 101 164 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 HETNAM K4Z 3-[3-[[4-[[4-[[4-[[4-[[(2~{R})-2-AZANIUMYL-4-[[1- HETNAM 2 K4Z METHYL-4-[[1-METHYL-4-[[1-METHYL-4-[(1-METHYLIMIDAZOL- HETNAM 3 K4Z 2-YL)CARBONYLAMINO]PYRROL-2-YL]CARBONYLAMINO]PYRROL-2- HETNAM 4 K4Z YL]CARBONYLAMINO]PYRROL-2- HETNAM 5 K4Z YL]CARBONYLAMINO]BUTANOYL]AMINO]-1-METHYL-IMIDAZOL-2- HETNAM 6 K4Z YL]CARBONYLAMINO]-1-METHYL-PYRROL-2-YL]CARBONYLAMINO]- HETNAM 7 K4Z 1-METHYL-PYRROL-2-YL]CARBONYLAMINO]-1-METHYL-PYRROL-2- HETNAM 8 K4Z YL]CARBONYLAMINO]PROPANOYLAMINO]PROPYL-DIMETHYL- HETNAM 9 K4Z AZANIUM FORMUL 1 DP 2(C10 H14 N5 O7 P) FORMUL 1 DZ 2(C10 H14 N3 O9 P) FORMUL 3 K4Z C58 H74 N22 O10 2+ 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 1.61 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 1.62 LINK O3' DZ B 20 P DA B 21 1555 1555 1.62 SITE 1 AC1 13 DP A 5 DT A 6 DA A 7 DZ A 8 SITE 2 AC1 13 DA A 9 DT A 10 DT B 16 DP B 17 SITE 3 AC1 13 DT B 18 DA B 19 DZ B 20 DA B 21 SITE 4 AC1 13 DT B 22 SITE 1 AC2 6 DA A 7 DZ A 8 DA A 9 DA B 15 SITE 2 AC2 6 DT B 18 K4Z B 101 SITE 1 AC3 6 DT A 6 DA A 7 DZ A 8 DT B 16 SITE 2 AC3 6 DA B 19 K4Z B 101 SITE 1 AC4 7 DT A 4 DP A 5 DT A 6 DA A 7 SITE 2 AC4 7 DT B 18 DA B 21 K4Z B 101 SITE 1 AC5 6 DA A 3 DT A 4 DP A 5 DA B 19 SITE 2 AC5 6 DT B 22 K4Z B 101 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