HEADER DNA 07-JUL-19 6KFI TITLE NMR SOLUTION STRUCTURE OF THE 1:1 COMPLEX OF TEL26 G-QUADRUPLEX AND A TITLE 2 TRIPODAL CATIONIC FLUORESCENT PROBE NBTE COMPND MOL_ID: 1; COMPND 2 MOLECULE: G-QUADRUPLEX DNA (26-MER); 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_TAXID: 9606 KEYWDS G-QUADRUPLEX DNA, PROBE, DNA EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR W.LIU,L.Y.LIU,Z.W.MAO REVDAT 3 01-MAY-24 6KFI 1 REMARK REVDAT 2 23-SEP-20 6KFI 1 JRNL REVDAT 1 08-JUL-20 6KFI 0 JRNL AUTH L.Y.LIU,W.LIU,K.N.WANG,B.C.ZHU,X.Y.XIA,L.N.JI,Z.W.MAO JRNL TITL QUANTITATIVE DETECTION OF G-QUADRUPLEX DNA IN LIVE CELLS JRNL TITL 2 BASED ON PHOTON COUNTS AND COMPLEX STRUCTURE DISCRIMINATION. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 59 9719 2020 JRNL REFN ESSN 1521-3773 JRNL PMID 32173994 JRNL DOI 10.1002/ANIE.202002422 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6KFI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300012877. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 278 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : 100; 100 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM TEL26, 1.0 MM NBTE, 100 REMARK 210 MM PATASSIUM, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 2D COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 DG A 5 C5' DG A 5 C4' 0.046 REMARK 500 1 DT A 7 C5 DT A 7 C7 0.052 REMARK 500 1 DT A 7 O3' DT A 8 P -0.102 REMARK 500 1 DT A 8 P DT A 8 O5' -0.077 REMARK 500 1 DT A 8 C5 DT A 8 C7 0.051 REMARK 500 1 DG A 12 C2' DG A 12 C1' 0.082 REMARK 500 1 DT A 13 C5 DT A 13 C7 0.052 REMARK 500 1 DT A 14 C5' DT A 14 C4' 0.083 REMARK 500 1 DT A 14 C5 DT A 14 C7 0.053 REMARK 500 1 DA A 15 C5' DA A 15 C4' 0.054 REMARK 500 1 DG A 16 C5' DG A 16 C4' 0.096 REMARK 500 1 DG A 18 C5' DG A 18 C4' 0.074 REMARK 500 1 DT A 19 C5 DT A 19 C7 0.052 REMARK 500 1 DT A 20 C5' DT A 20 C4' 0.045 REMARK 500 1 DT A 20 C5 DT A 20 C7 0.051 REMARK 500 1 DA A 21 C5' DA A 21 C4' 0.043 REMARK 500 1 DG A 23 C5' DG A 23 C4' 0.097 REMARK 500 2 DG A 4 C4 DG A 4 C5 0.044 REMARK 500 2 DG A 5 N7 DG A 5 C8 0.040 REMARK 500 2 DG A 6 N7 DG A 6 C8 0.041 REMARK 500 2 DT A 7 C6 DT A 7 N1 0.080 REMARK 500 2 DT A 7 O3' DT A 8 P -0.078 REMARK 500 2 DT A 8 C6 DT A 8 N1 0.069 REMARK 500 2 DA A 9 C5' DA A 9 C4' 0.044 REMARK 500 2 DG A 10 C5' DG A 10 C4' 0.047 REMARK 500 2 DG A 10 N7 DG A 10 C8 0.038 REMARK 500 2 DG A 12 C5' DG A 12 C4' 0.044 REMARK 500 2 DT A 13 C2' DT A 13 C1' 0.065 REMARK 500 2 DT A 13 C6 DT A 13 N1 0.092 REMARK 500 2 DT A 14 C5' DT A 14 C4' 0.059 REMARK 500 2 DT A 14 C4 DT A 14 C5 0.060 REMARK 500 2 DT A 14 C6 DT A 14 N1 0.087 REMARK 500 2 DG A 16 C5' DG A 16 C4' 0.091 REMARK 500 2 DG A 16 C4 DG A 16 C5 0.046 REMARK 500 2 DG A 17 C5' DG A 17 C4' 0.083 REMARK 500 2 DG A 17 N7 DG A 17 C8 0.048 REMARK 500 2 DG A 18 C5' DG A 18 C4' 0.051 REMARK 500 2 DT A 19 C4 DT A 19 C5 0.056 REMARK 500 2 DT A 19 C6 DT A 19 N1 0.083 REMARK 500 2 DT A 20 C6 DT A 20 N1 0.085 REMARK 500 2 DA A 21 C5' DA A 21 C4' 0.053 REMARK 500 2 DG A 22 N7 DG A 22 C8 0.038 REMARK 500 2 DG A 23 C5' DG A 23 C4' 0.070 REMARK 500 2 DG A 23 C4 DG A 23 C5 0.045 REMARK 500 2 DG A 24 C5' DG A 24 C4' 0.060 REMARK 500 2 DA A 25 N7 DA A 25 C8 0.044 REMARK 500 2 DA A 25 C6 DA A 25 N6 0.050 REMARK 500 2 DA A 26 C5' DA A 26 C4' 0.045 REMARK 500 3 DG A 5 P DG A 5 OP2 0.109 REMARK 500 3 DG A 5 P DG A 5 O5' -0.071 REMARK 500 REMARK 500 THIS ENTRY HAS 440 BOND DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL 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 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 1 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DA A 2 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DA A 2 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DA A 3 OP1 - P - OP2 ANGL. DEV. = -11.8 DEGREES REMARK 500 1 DA A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 4 OP1 - P - OP2 ANGL. DEV. = -13.8 DEGREES REMARK 500 1 DG A 4 O4' - C1' - C2' ANGL. DEV. = -7.9 DEGREES REMARK 500 1 DG A 4 N9 - C1' - C2' ANGL. DEV. = 12.0 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DG A 5 OP1 - P - OP2 ANGL. DEV. = -11.2 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 6 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 6 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DT A 7 O3' - P - O5' ANGL. DEV. = 15.3 DEGREES REMARK 500 1 DT A 7 C5' - C4' - O4' ANGL. DEV. = 8.5 DEGREES REMARK 500 1 DT A 7 C3' - O3' - P ANGL. DEV. = -7.3 DEGREES REMARK 500 1 DT A 8 P - O5' - C5' ANGL. DEV. = -16.0 DEGREES REMARK 500 1 DT A 8 C5' - C4' - O4' ANGL. DEV. = 9.2 DEGREES REMARK 500 1 DT A 8 C3' - C2' - C1' ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 9 O3' - P - O5' ANGL. DEV. = 23.2 DEGREES REMARK 500 1 DA A 9 OP1 - P - OP2 ANGL. DEV. = -19.6 DEGREES REMARK 500 1 DA A 9 O5' - P - OP1 ANGL. DEV. = -7.9 DEGREES REMARK 500 1 DA A 9 C1' - O4' - C4' ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DA A 9 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 9 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 10 N9 - C1' - C2' ANGL. DEV. = 20.0 DEGREES REMARK 500 1 DG A 10 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 10 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 11 O3' - P - OP1 ANGL. DEV. = 14.0 DEGREES REMARK 500 1 DG A 11 OP1 - P - OP2 ANGL. DEV. = -17.1 DEGREES REMARK 500 1 DG A 11 O5' - P - OP2 ANGL. DEV. = -14.8 DEGREES REMARK 500 1 DG A 11 N9 - C1' - C2' ANGL. DEV. = 11.8 DEGREES REMARK 500 1 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 11 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DG A 11 C3' - O3' - P ANGL. DEV. = 13.4 DEGREES REMARK 500 1 DG A 12 OP1 - P - OP2 ANGL. DEV. = -10.8 DEGREES REMARK 500 1 DG A 12 O5' - P - OP2 ANGL. DEV. = 8.4 DEGREES REMARK 500 1 DG A 12 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 12 C1' - O4' - C4' ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DG A 12 C3' - C2' - C1' ANGL. DEV. = 9.2 DEGREES REMARK 500 1 DG A 12 O4' - C1' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DG A 12 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1994 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 7 DT A 7 0.07 SIDE CHAIN REMARK 500 7 DG A 10 0.07 SIDE CHAIN REMARK 500 7 DT A 19 0.07 SIDE CHAIN REMARK 500 10 DG A 6 0.06 SIDE CHAIN REMARK 500 10 DT A 19 0.07 SIDE CHAIN REMARK 500 10 DA A 21 0.05 SIDE CHAIN REMARK 500 11 DG A 16 0.11 SIDE CHAIN REMARK 500 11 DT A 19 0.08 SIDE CHAIN REMARK 500 14 DA A 21 0.06 SIDE CHAIN REMARK 500 15 DA A 21 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue D6F A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36267 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF THE 1:1 COMPLEX OF TEL26 G-QUADRUPLEX AND REMARK 900 A TRIPODAL CATIONIC FLUORESCENT PROBE NBTE DBREF 6KFI A 1 26 PDB 6KFI 6KFI 1 26 SEQRES 1 A 26 DA DA DA DG DG DG DT DT DA DG DG DG DT SEQRES 2 A 26 DT DA DG DG DG DT DT DA DG DG DG DA DA HET D6F A 101 82 HETNAM D6F 4,4',4''-(NITRILOTRIS(BENZENE-4,1-DIYL))TRIS(1- HETNAM 2 D6F ETHYLPYRIDIN-1-IUM) IODIDE HETSYN D6F 4-(1-ETHYLPYRIDIN-1-IUM-4-YL)-N,N-BIS[4-(1- HETSYN 2 D6F ETHYLPYRIDIN-1-IUM-4-YL)PHENYL]ANILINE FORMUL 2 D6F C39 H39 N4 3+ SITE 1 AC1 4 DA A 3 DG A 4 DG A 10 DG A 22 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