HEADER DNA 09-AUG-23 8Q5Q TITLE D(ATTTC)3 DIMERIC STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*TP*TP*TP*(DNR) COMPND 3 P*AP*TP*TP*TP*CP*AP*TP*TP*TP*C)-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: 1 POLYMER "DNA (5'-D(*AP*TP*TP*TP*(DNR) COMPND 7 P*AP*TP*TP*TP*CP* AP*TP*TP*TP*C)-3')" 2 POLYMER "DNA (5'- COMPND 8 D(*AP*TP*TP*TP*(DNR)P*AP*TP*TP*TP*CP* AP*TP*TP*TP*C)-3')" SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS STEM-LOOP SEGMENT, INTERCALATED, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.TRAJKOVSKI,A.PASTORE,J.PLAVEC REVDAT 2 06-MAR-24 8Q5Q 1 JRNL REVDAT 1 07-FEB-24 8Q5Q 0 JRNL AUTH M.TRAJKOVSKI,A.PASTORE,J.PLAVEC JRNL TITL DIMERIC STRUCTURES OF DNA ATTTC REPEATS PROMOTED BY DIVALENT JRNL TITL 2 CATIONS. JRNL REF NUCLEIC ACIDS RES. V. 52 1591 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 38296828 JRNL DOI 10.1093/NAR/GKAE052 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 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 8Q5Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292132623. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 278 REMARK 210 PH : 6.0; 6.0 REMARK 210 IONIC STRENGTH : 20; 40 REMARK 210 PRESSURE : 1 BAR; 1 BAR REMARK 210 SAMPLE CONTENTS : 0.8 MM D(ATTTC)3, 90% H2O/10% REMARK 210 D2O; 0.8 MM [U-13C; U-15N] REMARK 210 D(ATTTC)3, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D 1H-13C HSQC; 2D 1H REMARK 210 -15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRFAM-SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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 DA A 1 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 1 N1 - C6 - N6 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DT A 2 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DA A 6 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA A 6 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA A 6 N1 - C6 - N6 ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC A 10 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DA A 11 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 11 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 12 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT A 13 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DT A 14 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DC A 15 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 15 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DA B 16 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA B 16 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA B 16 N1 - C6 - N6 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT B 18 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT B 18 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DA B 21 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA B 21 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA B 21 N1 - C6 - N6 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DT B 22 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT B 22 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT B 24 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DT B 24 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DC B 25 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC B 25 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DA B 26 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA B 26 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT B 27 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT B 27 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT B 28 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT B 28 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DT B 29 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 526 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34845 RELATED DB: BMRB REMARK 900 D(ATTTC)3 DIMERIC STRUCTURE DBREF 8Q5Q A 1 15 PDB 8Q5Q 8Q5Q 1 15 DBREF 8Q5Q B 16 30 PDB 8Q5Q 8Q5Q 16 30 SEQRES 1 A 15 DA DT DT DT DNR DA DT DT DT DC DA DT DT SEQRES 2 A 15 DT DC SEQRES 1 B 15 DA DT DT DT DNR DA DT DT DT DC DA DT DT SEQRES 2 B 15 DT DC HET DNR A 5 31 HET DNR B 20 31 HETNAM DNR 2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 DNR 2(C9 H15 N3 O7 P 1+) LINK O3' DT A 4 P DNR A 5 1555 1555 1.61 LINK O3' DNR A 5 P DA A 6 1555 1555 1.61 LINK O3' DT B 19 P DNR B 20 1555 1555 1.62 LINK O3' DNR B 20 P DA B 21 1555 1555 1.60 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL CONECT 103 127 CONECT 127 103 128 129 130 CONECT 128 127 CONECT 129 127 CONECT 130 127 131 CONECT 131 130 132 146 147 CONECT 132 131 133 144 148 CONECT 133 132 134 CONECT 134 133 135 143 149 CONECT 135 134 136 137 CONECT 136 135 142 150 CONECT 137 135 138 139 CONECT 138 137 CONECT 139 137 140 151 CONECT 140 139 141 142 CONECT 141 140 152 153 CONECT 142 136 140 154 CONECT 143 134 144 155 156 CONECT 144 132 143 145 157 CONECT 145 144 158 CONECT 146 131 CONECT 147 131 CONECT 148 132 CONECT 149 134 CONECT 150 136 CONECT 151 139 CONECT 152 141 CONECT 153 141 CONECT 154 142 CONECT 155 143 CONECT 156 143 CONECT 157 144 CONECT 158 145 CONECT 578 602 CONECT 602 578 603 604 605 CONECT 603 602 CONECT 604 602 CONECT 605 602 606 CONECT 606 605 607 621 622 CONECT 607 606 608 619 623 CONECT 608 607 609 CONECT 609 608 610 618 624 CONECT 610 609 611 612 CONECT 611 610 617 625 CONECT 612 610 613 614 CONECT 613 612 CONECT 614 612 615 626 CONECT 615 614 616 617 CONECT 616 615 627 628 CONECT 617 611 615 629 CONECT 618 609 619 630 631 CONECT 619 607 618 620 632 CONECT 620 619 633 CONECT 621 606 CONECT 622 606 CONECT 623 607 CONECT 624 609 CONECT 625 611 CONECT 626 614 CONECT 627 616 CONECT 628 616 CONECT 629 617 CONECT 630 618 CONECT 631 618 CONECT 632 619 CONECT 633 620 MASTER 144 0 2 0 0 0 0 6 594 2 66 4 END