HEADER DNA 24-SEP-24 9JO1 TITLE NMR SOLUTION STRUCTURE OF THE 2:1 BERBERINE-BLM-G4 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*TP*GP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*GP*AP*GP*GP*GP*AP*AP*T*)- COMPND 4 3'); COMPND 5 CHAIN: X; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS BLM PROMOTER, G-QUADRUPLEX, NMR SOLUTION STRUCTURE, DNA, BERBERINE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.B.WANG REVDAT 1 01-APR-26 9JO1 0 JRNL AUTH Y.Y.WANG,Y.T.BIAN,X.Y.CHEN,J.Z.LI,Y.S.LIU,L.Y.KONG,K.B.WANG JRNL TITL BLM G-QUADRUPLEX STABILIZERS SYNERGIZE WITH PARP INHIBITOR JRNL TITL 2 TO KILL BRCA WILD-TYPE COLON CANCER CELLS JRNL REF TO BE PUBLISHED JRNL REFN 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 9JO1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 01-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300051784. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 298; 308 REMARK 210 PH : 7; 7; 7 REMARK 210 IONIC STRENGTH : 50; 50; 50 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.93 MM NONE BLM_PU21T_BER, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HSQC; REMARK 210 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, X-PLOR NIH, 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 DT X 1 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG X 2 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA X 3 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA X 3 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA X 3 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG X 6 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA X 7 O4' - C1' - N9 ANGL. DEV. = 1.9 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. = 3.7 DEGREES REMARK 500 1 DA X 7 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DG X 8 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DG X 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC X 11 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG X 12 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG X 14 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA X 15 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA X 15 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA X 15 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG X 16 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG X 18 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA X 19 O4' - C1' - N9 ANGL. DEV. = 3.6 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. = -5.6 DEGREES REMARK 500 1 DA X 20 O4' - C1' - N9 ANGL. DEV. = 2.8 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. = 3.6 DEGREES REMARK 500 1 DA X 20 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DT X 21 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DT X 1 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DG X 2 O4' - C1' - N9 ANGL. DEV. = 2.7 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. = -5.2 DEGREES REMARK 500 2 DG X 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA X 7 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DA X 7 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA X 7 C5 - C6 - N1 ANGL. DEV. = 3.7 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. = 2.5 DEGREES REMARK 500 2 DG X 10 O4' - C1' - N9 ANGL. DEV. = 2.0 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. = 2.5 DEGREES REMARK 500 2 DG X 14 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DA X 15 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA X 15 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA X 15 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DG X 16 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DG X 18 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 288 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 X 21 0.07 SIDE CHAIN REMARK 500 3 DT X 21 0.06 SIDE CHAIN REMARK 500 4 DT X 21 0.06 SIDE CHAIN REMARK 500 5 DT X 21 0.07 SIDE CHAIN REMARK 500 6 DT X 21 0.07 SIDE CHAIN REMARK 500 9 DT X 21 0.06 SIDE CHAIN REMARK 500 10 DT X 21 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36695 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF FREE BLM PROMOTER G-QUADRUPLEX DBREF 9JO1 X 1 21 PDB 9JO1 9JO1 1 21 SEQRES 1 X 21 DT DG DA DG DG DG DA DG DG DG DC DG DG SEQRES 2 X 21 DG DA DG DG DG DA DA DT HET BER X 101 43 HET BER X 102 43 HETNAM BER BERBERINE FORMUL 2 BER 2(C20 H18 N O4 1+) 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 684 685 686 687 CONECT 685 684 688 689 CONECT 686 684 690 691 CONECT 687 684 692 709 CONECT 688 685 693 694 CONECT 689 685 695 710 CONECT 690 686 696 711 CONECT 691 686 694 712 713 CONECT 692 687 696 697 CONECT 693 688 698 714 CONECT 694 688 691 715 716 CONECT 695 689 698 699 CONECT 696 690 692 700 CONECT 697 692 701 717 CONECT 698 693 695 702 CONECT 699 695 703 CONECT 700 696 704 705 CONECT 701 697 704 718 CONECT 702 698 703 CONECT 703 699 702 719 720 CONECT 704 700 701 706 CONECT 705 700 707 CONECT 706 704 708 CONECT 707 705 721 722 723 CONECT 708 706 724 725 726 CONECT 709 687 CONECT 710 689 CONECT 711 690 CONECT 712 691 CONECT 713 691 CONECT 714 693 CONECT 715 694 CONECT 716 694 CONECT 717 697 CONECT 718 701 CONECT 719 703 CONECT 720 703 CONECT 721 707 CONECT 722 707 CONECT 723 707 CONECT 724 708 CONECT 725 708 CONECT 726 708 CONECT 727 728 729 730 CONECT 728 727 731 732 CONECT 729 727 733 734 CONECT 730 727 735 752 CONECT 731 728 736 737 CONECT 732 728 738 753 CONECT 733 729 739 754 CONECT 734 729 737 755 756 CONECT 735 730 739 740 CONECT 736 731 741 757 CONECT 737 731 734 758 759 CONECT 738 732 741 742 CONECT 739 733 735 743 CONECT 740 735 744 760 CONECT 741 736 738 745 CONECT 742 738 746 CONECT 743 739 747 748 CONECT 744 740 747 761 CONECT 745 741 746 CONECT 746 742 745 762 763 CONECT 747 743 744 749 CONECT 748 743 750 CONECT 749 747 751 CONECT 750 748 764 765 766 CONECT 751 749 767 768 769 CONECT 752 730 CONECT 753 732 CONECT 754 733 CONECT 755 734 CONECT 756 734 CONECT 757 736 CONECT 758 737 CONECT 759 737 CONECT 760 740 CONECT 761 744 CONECT 762 746 CONECT 763 746 CONECT 764 750 CONECT 765 750 CONECT 766 750 CONECT 767 751 CONECT 768 751 CONECT 769 751 MASTER 166 0 2 0 0 0 0 6 497 1 86 2 END