HEADER DNA 04-JUL-17 5OCZ TITLE FREE DNA_HAIRPIN POLYAMIDES STUDIES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*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 FREE- MINOR GROOVE BINDERS- POLYAMIDES, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR G.PADRONI,J.PARKINSON,G.A.BURLEY REVDAT 6 15-MAY-24 5OCZ 1 REMARK REVDAT 5 08-MAY-19 5OCZ 1 REMARK REVDAT 4 07-FEB-18 5OCZ 1 SOURCE REVDAT 3 24-JAN-18 5OCZ 1 JRNL REVDAT 2 13-DEC-17 5OCZ 1 JRNL REVDAT 1 06-DEC-17 5OCZ 0 JRNL AUTH G.PADRONI,J.A.PARKINSON,K.R.FOX,G.A.BURLEY JRNL TITL STRUCTURAL BASIS OF DNA DUPLEX DISTORTION INDUCED BY JRNL TITL 2 THIAZOLE-CONTAINING HAIRPIN POLYAMIDES. JRNL REF NUCLEIC ACIDS RES. V. 46 42 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 29194552 JRNL DOI 10.1093/NAR/GKX1211 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5OCZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1200005590. 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 : 100MM PHOSHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.3 MM NA DNA (5' REMARK 210 -D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 90% H2O/10% D2O; REMARK 210 1.3 MM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 99% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY; 2D 1H-13C HSQC; 31P- REMARK 210 H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, TOPSPIN, MARDIGRAS, REMARK 210 AMBER, UCSF CHIMERA REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA A 7 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 7 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 7 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DC A 8 C5' - C4' - O4' ANGL. DEV. = 6.6 DEGREES REMARK 500 1 DC A 8 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DC A 8 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DC A 8 N3 - C2 - O2 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DA A 9 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.5 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. = -6.0 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC A 11 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DA B 15 O4' - C1' - N9 ANGL. DEV. = 3.2 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. = -5.1 DEGREES REMARK 500 1 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG B 17 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG B 17 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT B 18 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA B 19 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA B 19 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA B 19 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA B 19 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DC B 20 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DC B 20 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC B 20 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DA B 21 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DA B 21 C4 - C5 - C6 ANGL. DEV. = -3.5 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. = -6.0 DEGREES REMARK 500 1 DT B 22 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DC B 23 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC B 23 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 485 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 0.06 SIDE CHAIN REMARK 500 1 DT A 10 0.11 SIDE CHAIN REMARK 500 1 DT B 22 0.12 SIDE CHAIN REMARK 500 1 DG B 24 0.06 SIDE CHAIN REMARK 500 2 DT A 4 0.07 SIDE CHAIN REMARK 500 2 DT A 6 0.07 SIDE CHAIN REMARK 500 2 DT A 10 0.10 SIDE CHAIN REMARK 500 2 DG A 12 0.09 SIDE CHAIN REMARK 500 2 DT B 18 0.06 SIDE CHAIN REMARK 500 2 DT B 22 0.07 SIDE CHAIN REMARK 500 2 DG B 24 0.07 SIDE CHAIN REMARK 500 3 DT A 10 0.10 SIDE CHAIN REMARK 500 3 DG A 12 0.06 SIDE CHAIN REMARK 500 3 DT B 16 0.07 SIDE CHAIN REMARK 500 3 DT B 18 0.09 SIDE CHAIN REMARK 500 3 DC B 20 0.07 SIDE CHAIN REMARK 500 3 DT B 22 0.09 SIDE CHAIN REMARK 500 3 DG B 24 0.06 SIDE CHAIN REMARK 500 4 DT A 10 0.11 SIDE CHAIN REMARK 500 4 DG A 12 0.07 SIDE CHAIN REMARK 500 4 DC B 20 0.07 SIDE CHAIN REMARK 500 4 DT B 22 0.07 SIDE CHAIN REMARK 500 4 DG B 24 0.06 SIDE CHAIN REMARK 500 5 DT A 10 0.10 SIDE CHAIN REMARK 500 5 DG A 12 0.07 SIDE CHAIN REMARK 500 5 DT B 22 0.12 SIDE CHAIN REMARK 500 5 DG B 24 0.06 SIDE CHAIN REMARK 500 6 DG A 5 0.07 SIDE CHAIN REMARK 500 6 DT A 10 0.08 SIDE CHAIN REMARK 500 6 DG A 12 0.07 SIDE CHAIN REMARK 500 6 DT B 22 0.10 SIDE CHAIN REMARK 500 6 DG B 24 0.08 SIDE CHAIN REMARK 500 7 DT A 10 0.12 SIDE CHAIN REMARK 500 7 DG A 12 0.08 SIDE CHAIN REMARK 500 7 DG B 17 0.07 SIDE CHAIN REMARK 500 7 DC B 20 0.07 SIDE CHAIN REMARK 500 7 DT B 22 0.09 SIDE CHAIN REMARK 500 7 DG B 24 0.09 SIDE CHAIN REMARK 500 8 DT A 6 0.10 SIDE CHAIN REMARK 500 8 DT A 10 0.12 SIDE CHAIN REMARK 500 8 DG A 12 0.09 SIDE CHAIN REMARK 500 8 DC B 20 0.07 SIDE CHAIN REMARK 500 8 DT B 22 0.13 SIDE CHAIN REMARK 500 8 DG B 24 0.07 SIDE CHAIN REMARK 500 9 DT A 6 0.07 SIDE CHAIN REMARK 500 9 DT A 10 0.12 SIDE CHAIN REMARK 500 9 DG A 12 0.07 SIDE CHAIN REMARK 500 9 DT B 18 0.06 SIDE CHAIN REMARK 500 9 DT B 22 0.08 SIDE CHAIN REMARK 500 9 DG B 24 0.08 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 56 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34156 RELATED DB: BMRB REMARK 900 FREE DNA_HAIRPIN POLYAMIDES STUDIES DBREF 5OCZ A 1 12 PDB 5OCZ 5OCZ 1 12 DBREF 5OCZ B 13 24 PDB 5OCZ 5OCZ 13 24 SEQRES 1 A 12 DCZ DG DA DT DG DT DA DC DA DT DC DG SEQRES 1 B 12 DCZ DG DA DT DG DT DA DC DA DT DC DG HET DCZ A 1 28 HET DCZ B 13 28 HETNAM DCZ 2'-DEOXYCYTIDINE FORMUL 1 DCZ 2(C9 H13 N3 O4) LINK O3'DDCZ A 1 P DG A 2 1555 1555 1.62 LINK O3'DDCZ B 13 P DG B 14 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 HETATM 1 N1 DDCZ A 1 31.233 8.760 12.578 1.00 0.00 N HETATM 2 C2 DDCZ A 1 32.124 9.636 11.934 1.00 0.00 C HETATM 3 N3 DDCZ A 1 31.694 10.809 11.405 1.00 0.00 N HETATM 4 C4 DDCZ A 1 30.410 11.095 11.478 1.00 0.00 C HETATM 5 C5 DDCZ A 1 29.445 10.229 12.053 1.00 0.00 C HETATM 6 C6 DDCZ A 1 29.889 9.065 12.587 1.00 0.00 C HETATM 7 O2 DDCZ A 1 33.327 9.391 11.813 1.00 0.00 O HETATM 8 N4 DDCZ A 1 30.047 12.234 10.965 1.00 0.00 N HETATM 9 C1'DDCZ A 1 31.768 7.503 13.198 1.00 0.00 C HETATM 10 C2'DDCZ A 1 31.134 7.124 14.549 1.00 0.00 C HETATM 11 C3'DDCZ A 1 30.842 5.624 14.458 1.00 0.00 C HETATM 12 C4'DDCZ A 1 30.769 5.398 12.942 1.00 0.00 C HETATM 13 O4'DDCZ A 1 31.558 6.409 12.317 1.00 0.00 O HETATM 14 O3'DDCZ A 1 31.841 4.794 15.037 1.00 0.00 O HETATM 15 C5'DDCZ A 1 29.309 5.406 12.448 1.00 0.00 C HETATM 16 O5'DDCZ A 1 29.203 5.457 11.026 1.00 0.00 O HETATM 17 H5 DDCZ A 1 28.392 10.468 12.079 1.00 0.00 H HETATM 18 H6 DDCZ A 1 29.178 8.376 13.023 1.00 0.00 H HETATM 19 HN41DDCZ A 1 29.089 12.527 11.043 1.00 0.00 H HETATM 20 HN42DDCZ A 1 30.777 12.866 10.656 1.00 0.00 H HETATM 21 H1'DDCZ A 1 32.846 7.614 13.358 1.00 0.00 H HETATM 22 H2'1DDCZ A 1 30.210 7.661 14.747 1.00 0.00 H HETATM 23 H2'2DDCZ A 1 31.823 7.348 15.357 1.00 0.00 H HETATM 24 H3'DDCZ A 1 29.873 5.401 14.910 1.00 0.00 H HETATM 25 H4'DDCZ A 1 31.195 4.419 12.712 1.00 0.00 H HETATM 26 H5'1DDCZ A 1 28.823 4.500 12.815 1.00 0.00 H HETATM 27 H5'2DDCZ A 1 28.784 6.257 12.881 1.00 0.00 H HETATM 28 HO51DDCZ A 1 29.813 4.803 10.624 1.00 0.00 H