HEADER DNA 29-DEC-21 7WGW TITLE NMR SOLUTION STRUCTURE OF A CGMP FILL-IN VACANCY G-QUADRUPLEX FORMED TITLE 2 IN THE OXIDIZED BLM GENE PROMOTER COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (20-MER); COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS 8-OXO-7, 8-DIHYDROGUANINE, G-QUADRUPLEX, BLOOM SYNDROME PROTEIN, KEYWDS 2 GUANINE METABOLITE, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.B.WANG,Y.LIU,Y.LI,J.LI,J.DICKERHOFF,M.H.YANG,D.YANG,L.Y.KONG REVDAT 2 15-MAY-24 7WGW 1 REMARK REVDAT 1 18-MAY-22 7WGW 0 JRNL AUTH K.B.WANG,Y.LIU,Y.LI,J.DICKERHOFF,J.LI,M.H.YANG,D.YANG, JRNL AUTH 2 L.Y.KONG JRNL TITL OXIDATIVE DAMAGE INDUCES A VACANCY G-QUADRUPLEX THAT BINDS JRNL TITL 2 GUANINE METABOLITES: SOLUTION STRUCTURE OF A CGMP FILL-IN JRNL TITL 3 VACANCY G-QUADRUPLEX IN THE OXIDIZED BLM GENE PROMOTER. JRNL REF J.AM.CHEM.SOC. V. 144 6361 2022 JRNL REFN ESSN 1520-5126 JRNL PMID 35352895 JRNL DOI 10.1021/JACS.2C00435 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 7WGW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300026271. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 278; 283; 288; 303; 310 REMARK 210 PH : 7.0; 7.0; 7.0; 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 50; 50; 50; 50; 50; 50 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM; 1 ATM; 1 REMARK 210 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.2 MM NONE BLM_G18O, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D DQF-COSY; 2D REMARK 210 1H-13C HSQC; 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, TOPSPIN, NMRFAM REMARK 210 -SPARKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 X 2 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA X 2 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA X 2 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DA X 3 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA X 3 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA X 3 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA X 3 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DA X 7 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA X 7 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA X 7 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DG X 9 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG X 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC X 11 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DC X 11 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG X 12 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DG X 13 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG X 14 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA X 15 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DA X 15 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA X 15 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DG X 16 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG X 17 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA X 19 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA X 19 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA X 19 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA X 19 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DA X 20 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA X 20 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA X 20 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA X 20 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DA X 2 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DA X 2 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA X 2 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DA X 3 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DA X 3 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 DA X 3 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA X 3 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 DA X 7 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DA X 7 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA X 7 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 DG X 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG X 9 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG X 10 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC X 11 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC X 11 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DG X 12 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DG X 13 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DG X 14 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA X 15 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DA X 15 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 293 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 4 DG X 13 0.05 SIDE CHAIN REMARK 500 5 DG X 14 0.07 SIDE CHAIN REMARK 500 6 DG X 4 0.06 SIDE CHAIN REMARK 500 6 DG X 13 0.06 SIDE CHAIN REMARK 500 8 DG X 14 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36467 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF A CGMP FILL-IN VACANCY G-QUADRUPLEX REMARK 900 FORMED IN THE OXIDIZED BLM GENE PROMOTER DBREF 7WGW X 1 20 PDB 7WGW 7WGW 1 20 SEQRES 1 X 20 THM DA DA DG DG DG DA DG DG DG DC DG DG SEQRES 2 X 20 DG DA DG DG 8OG DA DA HET THM X 1 30 HET 8OG X 18 34 HET PCG X 101 34 HETNAM THM THYMIDINE HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM PCG CYCLIC GUANOSINE MONOPHOSPHATE HETSYN THM DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 1 THM C10 H14 N2 O5 FORMUL 1 8OG C10 H14 N5 O8 P FORMUL 2 PCG C10 H12 N5 O7 P LINK O3' THM X 1 P DA X 2 1555 1555 1.62 LINK O3' DG X 17 P 8OG X 18 1555 1555 1.62 LINK O3' 8OG X 18 P DA X 19 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 X 1 12.403 22.629 19.283 1.00 0.00 O HETATM 2 C5' THM X 1 11.825 21.534 18.569 1.00 0.00 C HETATM 3 C4' THM X 1 12.844 20.448 18.164 1.00 0.00 C HETATM 4 O4' THM X 1 13.780 20.975 17.224 1.00 0.00 O HETATM 5 C3' THM X 1 13.642 19.871 19.348 1.00 0.00 C HETATM 6 O3' THM X 1 13.785 18.462 19.164 1.00 0.00 O HETATM 7 C2' THM X 1 14.968 20.624 19.230 1.00 0.00 C HETATM 8 C1' THM X 1 15.097 20.773 17.715 1.00 0.00 C HETATM 9 N1 THM X 1 15.979 21.887 17.266 1.00 0.00 N HETATM 10 C2 THM X 1 16.993 21.599 16.341 1.00 0.00 C HETATM 11 O2 THM X 1 17.219 20.476 15.890 1.00 0.00 O HETATM 12 N3 THM X 1 17.752 22.658 15.898 1.00 0.00 N HETATM 13 C4 THM X 1 17.569 23.980 16.240 1.00 0.00 C HETATM 14 O4 THM X 1 18.292 24.829 15.717 1.00 0.00 O HETATM 15 C5 THM X 1 16.493 24.219 17.203 1.00 0.00 C HETATM 16 C5M THM X 1 16.171 25.636 17.654 1.00 0.00 C HETATM 17 C6 THM X 1 15.755 23.185 17.688 1.00 0.00 C HETATM 18 HO5' THM X 1 11.696 23.242 19.572 1.00 0.00 H HETATM 19 H5'1 THM X 1 11.334 21.903 17.665 1.00 0.00 H HETATM 20 H5'2 THM X 1 11.058 21.066 19.190 1.00 0.00 H HETATM 21 H4' THM X 1 12.287 19.635 17.693 1.00 0.00 H HETATM 22 H3' THM X 1 13.146 20.091 20.296 1.00 0.00 H HETATM 23 H2'1 THM X 1 14.886 21.591 19.725 1.00 0.00 H HETATM 24 H2'2 THM X 1 15.803 20.069 19.646 1.00 0.00 H HETATM 25 H1' THM X 1 15.469 19.821 17.328 1.00 0.00 H HETATM 26 HN3 THM X 1 18.481 22.451 15.242 1.00 0.00 H HETATM 27 HM51 THM X 1 15.397 25.640 18.423 1.00 0.00 H HETATM 28 HM52 THM X 1 15.831 26.219 16.796 1.00 0.00 H HETATM 29 HM53 THM X 1 17.072 26.106 18.049 1.00 0.00 H HETATM 30 H6 THM X 1 14.943 23.383 18.379 1.00 0.00 H