HEADER DNA 18-OCT-17 6ERL TITLE QUADRUPLEX WITH FLIPPED TETRAD FORMED BY THE C-MYC PROMOTER SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CMBR-481317; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS QUADRUPLEX, G4, 8-BROMO-GUANOSINE, TETRAD FLIP, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR B.KARG,K.WEISZ REVDAT 4 19-JUN-24 6ERL 1 REMARK REVDAT 3 14-JUN-23 6ERL 1 REMARK REVDAT 2 08-MAY-19 6ERL 1 REMARK REVDAT 1 13-JUN-18 6ERL 0 JRNL AUTH B.KARG,K.WEISZ JRNL TITL LOOP LENGTH AFFECTS SYN-ANTI CONFORMATIONAL REARRANGEMENTS JRNL TITL 2 IN PARALLEL G-QUADRUPLEXES. JRNL REF CHEMISTRY 2018 JRNL REFN ISSN 1521-3765 JRNL PMID 29756658 JRNL DOI 10.1002/CHEM.201801851 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, XPLOR-NIH, AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN (AMBER), SCHWIETERS, REMARK 3 KUSZEWSKI, TJANDRA AND CLORE (XPLOR-NIH), CASE, REMARK 3 DARDEN, CHEATHAM III, SIMMERLING, WANG, DUKE, LUO, REMARK 3 ... AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6ERL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1200006818. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 10 MM NA POTASSIUM PHOSPHATE, REMARK 210 90% H2O/10% D2O; 10 MM NA REMARK 210 POTASSIUM PHOSPHATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D DQF-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 : CCPNMR ANALYSIS REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 22.0 KCAL/MOL 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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES 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. = 4.8 DEGREES REMARK 500 1 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 3 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 11 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA A 12 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA A 12 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 12 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 16 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT A 20 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 21 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA A 21 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 21 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DA A 22 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA A 22 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA A 22 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 22 N1 - C6 - N6 ANGL. DEV. = -6.8 DEGREES REMARK 500 2 DT A 1 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 8.5 DEGREES REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DA A 3 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 DT A 11 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DT A 11 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DA A 12 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA A 12 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA A 12 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DG A 14 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT A 16 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 DT A 16 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DG A 18 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DG A 19 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DT A 20 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DT A 20 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 20 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 282 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 1 0.06 SIDE CHAIN REMARK 500 1 DG A 10 0.06 SIDE CHAIN REMARK 500 1 DA A 22 0.10 SIDE CHAIN REMARK 500 2 DT A 1 0.08 SIDE CHAIN REMARK 500 2 DG A 2 0.07 SIDE CHAIN REMARK 500 2 DG A 5 0.07 SIDE CHAIN REMARK 500 2 DG A 6 0.07 SIDE CHAIN REMARK 500 2 DG A 10 0.08 SIDE CHAIN REMARK 500 2 DG A 19 0.06 SIDE CHAIN REMARK 500 2 DT A 20 0.07 SIDE CHAIN REMARK 500 2 DA A 22 0.06 SIDE CHAIN REMARK 500 3 DG A 5 0.07 SIDE CHAIN REMARK 500 3 DG A 14 0.06 SIDE CHAIN REMARK 500 3 DG A 15 0.06 SIDE CHAIN REMARK 500 3 DA A 22 0.10 SIDE CHAIN REMARK 500 4 DG A 6 0.07 SIDE CHAIN REMARK 500 4 DG A 15 0.06 SIDE CHAIN REMARK 500 4 DG A 19 0.06 SIDE CHAIN REMARK 500 5 DG A 10 0.10 SIDE CHAIN REMARK 500 6 DG A 6 0.05 SIDE CHAIN REMARK 500 6 DG A 19 0.06 SIDE CHAIN REMARK 500 7 DG A 19 0.07 SIDE CHAIN REMARK 500 8 DG A 5 0.05 SIDE CHAIN REMARK 500 8 DG A 6 0.07 SIDE CHAIN REMARK 500 8 DG A 10 0.11 SIDE CHAIN REMARK 500 8 DG A 19 0.06 SIDE CHAIN REMARK 500 9 DG A 5 0.06 SIDE CHAIN REMARK 500 9 DG A 10 0.09 SIDE CHAIN REMARK 500 10 DG A 10 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34186 RELATED DB: BMRB REMARK 900 QUADRUPLEX WITH FLIPPED TETRAD FORMED BY THE C-MYC PROMOTER SEQUENCE DBREF 6ERL A 1 22 PDB 6ERL 6ERL 1 22 SEQRES 1 A 22 DT DG DA BGM DG DG DT BGM DG DG DT DA BGM SEQRES 2 A 22 DG DG DT BGM DG DG DT DA DA HET BGM A 4 33 HET BGM A 8 33 HET BGM A 13 33 HET BGM A 17 33 HETNAM BGM 8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE FORMUL 1 BGM 4(C10 H13 BR N5 O7 P) LINK O3' DA A 3 P BGM A 4 1555 1555 1.61 LINK O3' BGM A 4 P DG A 5 1555 1555 1.61 LINK O3' DT A 7 P BGM A 8 1555 1555 1.61 LINK O3' BGM A 8 P DG A 9 1555 1555 1.61 LINK O3' DA A 12 P BGM A 13 1555 1555 1.62 LINK O3' BGM A 13 P DG A 14 1555 1555 1.61 LINK O3' DT A 16 P BGM A 17 1555 1555 1.62 LINK O3' BGM A 17 P DG A 18 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