HEADER DNA 29-MAR-21 7O1H TITLE HYBRID-2R QUADRUPLEX-DUPLEX WITH (-P-P-L) TOPOLOGY AND 3 SYN RESIDUES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (31-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS QUADRUPLEX-DUPLEX HYBRID, HYBRID TOPOLOGY, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.MOHR,Y.M.VIANNEY,K.WEISZ REVDAT 3 19-JUN-24 7O1H 1 REMARK REVDAT 2 28-JUL-21 7O1H 1 JRNL REVDAT 1 19-MAY-21 7O1H 0 JRNL AUTH S.MOHR,J.JANA,Y.M.VIANNEY,K.WEISZ JRNL TITL EXPANDING THE TOPOLOGICAL LANDSCAPE BY A G-COLUMN FLIP OF A JRNL TITL 2 PARALLEL G-QUADRUPLEX. JRNL REF CHEMISTRY V. 27 10437 2021 JRNL REFN ISSN 0947-6539 JRNL PMID 33955615 JRNL DOI 10.1002/CHEM.202101181 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 16 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 7O1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1292114972. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.3 MM NO DNA (31-MER), 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HSQC REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS 2.4.2, TOPSPIN REMARK 210 4.0.7, X-PLOR NIH 3.0.3 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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. = 3.9 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 11 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA A 15 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 15 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 15 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DC A 16 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC A 18 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DC A 20 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC A 20 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DA A 21 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DA A 21 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 21 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 21 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DA A 21 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC A 23 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DT A 25 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG A 27 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 1 DG A 27 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DT A 29 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT A 29 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA A 30 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 30 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA A 30 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA A 31 O4' - C1' - N9 ANGL. DEV. = 6.8 DEGREES REMARK 500 1 DA A 31 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 31 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 31 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 1.9 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. = 3.5 DEGREES REMARK 500 2 DA A 3 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DT A 11 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 387 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 DA A 31 0.06 SIDE CHAIN REMARK 500 3 DT A 29 0.07 SIDE CHAIN REMARK 500 4 DG A 4 0.05 SIDE CHAIN REMARK 500 4 DA A 31 0.11 SIDE CHAIN REMARK 500 5 DA A 3 0.06 SIDE CHAIN REMARK 500 5 DG A 12 0.06 SIDE CHAIN REMARK 500 5 DA A 21 0.07 SIDE CHAIN REMARK 500 6 DG A 2 0.06 SIDE CHAIN REMARK 500 6 DC A 18 0.07 SIDE CHAIN REMARK 500 7 DC A 18 0.08 SIDE CHAIN REMARK 500 8 DG A 2 0.07 SIDE CHAIN REMARK 500 8 DG A 6 0.07 SIDE CHAIN REMARK 500 8 DC A 18 0.07 SIDE CHAIN REMARK 500 9 DG A 2 0.09 SIDE CHAIN REMARK 500 9 DG A 13 0.06 SIDE CHAIN REMARK 500 9 DA A 30 0.07 SIDE CHAIN REMARK 500 9 DA A 31 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34615 RELATED DB: BMRB REMARK 900 HYBRID-2R QUADRUPLEX-DUPLEX WITH (-P-P-L) TOPOLOGY AND 3 SYN REMARK 900 RESIDUES DBREF 7O1H A 1 31 PDB 7O1H 7O1H 1 31 SEQRES 1 A 31 THM DG DA DG DG DG DT DG DG DG DT DG DG SEQRES 2 A 31 DG DA DC DG DC DG DC DA DG DC DG DT BGM SEQRES 3 A 31 DG BGM DT DA DA HET THM A 1 30 HET BGM A 26 33 HET BGM A 28 33 HETNAM THM THYMIDINE HETNAM BGM 8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE HETSYN THM DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE FORMUL 1 THM C10 H14 N2 O5 FORMUL 1 BGM 2(C10 H13 BR N5 O7 P) LINK O3' THM A 1 P DG A 2 1555 1555 1.62 LINK O3' DT A 25 P BBGM A 26 1555 1555 1.61 LINK O3'BBGM A 26 P DG A 27 1555 1555 1.61 LINK O3' DG A 27 P BBGM A 28 1555 1555 1.63 LINK O3'BBGM A 28 P DT A 29 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 O5' THM A 1 42.394 28.091 25.282 1.00 0.00 O HETATM 2 C5' THM A 1 41.832 29.021 26.206 1.00 0.00 C HETATM 3 C4' THM A 1 41.381 28.367 27.524 1.00 0.00 C HETATM 4 O4' THM A 1 40.416 27.348 27.308 1.00 0.00 O HETATM 5 C3' THM A 1 42.532 27.702 28.297 1.00 0.00 C HETATM 6 O3' THM A 1 43.090 28.614 29.238 1.00 0.00 O HETATM 7 C2' THM A 1 41.860 26.478 28.935 1.00 0.00 C HETATM 8 C1' THM A 1 40.402 26.559 28.483 1.00 0.00 C HETATM 9 N1 THM A 1 39.819 25.210 28.250 1.00 0.00 N HETATM 10 C2 THM A 1 39.078 24.626 29.284 1.00 0.00 C HETATM 11 O2 THM A 1 38.813 25.205 30.335 1.00 0.00 O HETATM 12 N3 THM A 1 38.655 23.328 29.104 1.00 0.00 N HETATM 13 C4 THM A 1 38.925 22.544 28.004 1.00 0.00 C HETATM 14 O4 THM A 1 38.517 21.384 27.990 1.00 0.00 O HETATM 15 C5 THM A 1 39.708 23.209 26.955 1.00 0.00 C HETATM 16 C5M THM A 1 40.066 22.466 25.676 1.00 0.00 C HETATM 17 C6 THM A 1 40.121 24.496 27.108 1.00 0.00 C HETATM 18 HO5' THM A 1 41.691 27.485 24.977 1.00 0.00 H HETATM 19 H5'1 THM A 1 40.975 29.518 25.750 1.00 0.00 H HETATM 20 H5'2 THM A 1 42.575 29.785 26.440 1.00 0.00 H HETATM 21 H4' THM A 1 40.941 29.139 28.159 1.00 0.00 H HETATM 22 H3' THM A 1 43.300 27.364 27.599 1.00 0.00 H HETATM 23 H2'1 THM A 1 42.336 25.571 28.560 1.00 0.00 H HETATM 24 H2'2 THM A 1 41.904 26.497 30.023 1.00 0.00 H HETATM 25 H1' THM A 1 39.831 27.086 29.255 1.00 0.00 H HETATM 26 HN3 THM A 1 38.160 22.888 29.866 1.00 0.00 H HETATM 27 HM51 THM A 1 40.806 21.694 25.904 1.00 0.00 H HETATM 28 HM52 THM A 1 40.468 23.153 24.926 1.00 0.00 H HETATM 29 HM53 THM A 1 39.170 21.983 25.276 1.00 0.00 H HETATM 30 H6 THM A 1 40.701 24.976 26.329 1.00 0.00 H