HEADER DNA 10-NOV-16 5MCR TITLE QUADRUPLEX WITH FLIPPED TETRAD FORMED BY AN ARTIFICIAL SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARTIFICIAL QUADRUPLEX WITH PROPELLER, DIAGONAL AND LATERAL COMPND 3 LOOP; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS G-QUADRUPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.DICKERHOFF,L.HAASE,W.LANGEL,K.WEISZ REVDAT 4 15-MAY-24 5MCR 1 REMARK REVDAT 3 08-MAY-19 5MCR 1 REMARK REVDAT 2 31-MAY-17 5MCR 1 JRNL REVDAT 1 19-APR-17 5MCR 0 JRNL AUTH J.DICKERHOFF,L.HAASE,W.LANGEL,K.WEISZ JRNL TITL TRACING EFFECTS OF FLUORINE SUBSTITUTIONS ON G-QUADRUPLEX JRNL TITL 2 CONFORMATIONAL CHANGES. JRNL REF ACS CHEM. BIOL. V. 12 1308 2017 JRNL REFN ESSN 1554-8937 JRNL PMID 28318229 JRNL DOI 10.1021/ACSCHEMBIO.6B01096 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.39, AMBER 14 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (XPLOR REMARK 3 -NIH), CASE, DARDEN, CHEATHAM III, SIMMERLING, REMARK 3 WANG, DUKE, LUO, ... AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5MCR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1200002238. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.9 MM DNA, 10.0 MM POTASSIUM REMARK 210 PHOSPHATE, 90% H2O/10% D2O; 0.9 REMARK 210 MM DNA, 10.0 MM POTASSIUM REMARK 210 PHOSPHATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HSQC REMARK 210 AROMATIC; 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 2.1 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 : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 4 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT A 5 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DA A 9 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 9 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC A 10 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DA A 11 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 11 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DA A 11 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DC A 12 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DA A 13 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DA A 13 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA A 13 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 13 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DG A 14 O4' - C1' - N9 ANGL. DEV. = 7.2 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 15 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA A 18 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 18 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC A 19 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DC A 19 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DA A 4 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA A 9 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 DA A 9 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA A 9 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC A 10 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DA A 11 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 DA A 11 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DA A 11 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DA A 11 N1 - C6 - N6 ANGL. DEV. = -6.4 DEGREES REMARK 500 2 DC A 12 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 DC A 12 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 327 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 DG A 7 0.07 SIDE CHAIN REMARK 500 1 DA A 11 0.06 SIDE CHAIN REMARK 500 1 DA A 13 0.06 SIDE CHAIN REMARK 500 2 DG A 3 0.06 SIDE CHAIN REMARK 500 2 DG A 7 0.08 SIDE CHAIN REMARK 500 2 DC A 10 0.07 SIDE CHAIN REMARK 500 2 DA A 13 0.06 SIDE CHAIN REMARK 500 2 DG A 21 0.05 SIDE CHAIN REMARK 500 3 DG A 7 0.06 SIDE CHAIN REMARK 500 3 DA A 9 0.07 SIDE CHAIN REMARK 500 3 DA A 11 0.12 SIDE CHAIN REMARK 500 3 DC A 19 0.08 SIDE CHAIN REMARK 500 3 DG A 21 0.08 SIDE CHAIN REMARK 500 4 DG A 7 0.06 SIDE CHAIN REMARK 500 4 DG A 8 0.06 SIDE CHAIN REMARK 500 4 DA A 11 0.08 SIDE CHAIN REMARK 500 4 DC A 19 0.08 SIDE CHAIN REMARK 500 6 DG A 8 0.07 SIDE CHAIN REMARK 500 6 DA A 11 0.08 SIDE CHAIN REMARK 500 6 DG A 16 0.05 SIDE CHAIN REMARK 500 6 DC A 19 0.06 SIDE CHAIN REMARK 500 7 DG A 7 0.06 SIDE CHAIN REMARK 500 7 DA A 9 0.05 SIDE CHAIN REMARK 500 7 DA A 11 0.11 SIDE CHAIN REMARK 500 8 DT A 5 0.07 SIDE CHAIN REMARK 500 8 DG A 8 0.06 SIDE CHAIN REMARK 500 8 DA A 9 0.06 SIDE CHAIN REMARK 500 8 DA A 11 0.08 SIDE CHAIN REMARK 500 9 DC A 12 0.09 SIDE CHAIN REMARK 500 9 DA A 13 0.11 SIDE CHAIN REMARK 500 9 DC A 19 0.07 SIDE CHAIN REMARK 500 10 DT A 5 0.06 SIDE CHAIN REMARK 500 10 DA A 13 0.08 SIDE CHAIN REMARK 500 10 DC A 19 0.07 SIDE CHAIN REMARK 500 10 DG A 22 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34063 RELATED DB: BMRB REMARK 900 QUADRUPLEX WITH FLIPPED TETRAD FORMED BY AN ARTIFICIAL SEQUENCE DBREF 5MCR A 1 22 PDB 5MCR 5MCR 1 22 SEQRES 1 A 22 GF0 DG DG DA DT GF2 DG DG DA DC DA DC DA SEQRES 2 A 22 DG DG DG DG DA DC GF2 DG DG HET GF0 A 1 31 HET GF2 A 6 33 HET GF2 A 20 33 HETNAM GF0 2'-DEOXY-2'-FLUOROGUANOSINE HETNAM GF2 2'-DEOXY-2'-FLUOROGUANOSINE 5'-(DIHYDROGEN PHOSPHATE) FORMUL 1 GF0 C10 H12 F N5 O4 FORMUL 1 GF2 2(C10 H13 F N5 O7 P) LINK O3' GF0 A 1 P DG A 2 1555 1555 1.60 LINK O3' DT A 5 P GF2 A 6 1555 1555 1.62 LINK O3' GF2 A 6 P DG A 7 1555 1555 1.61 LINK O3' DC A 19 P GF2 A 20 1555 1555 1.61 LINK O3' GF2 A 20 P DG A 21 1555 1555 1.62 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 F GF0 A 1 31.418 24.117 28.450 1.00 0.00 F HETATM 2 N1 GF0 A 1 33.610 28.186 23.870 1.00 0.00 N HETATM 3 C2 GF0 A 1 33.013 28.028 25.078 1.00 0.00 C HETATM 4 N2 GF0 A 1 32.519 29.093 25.657 1.00 0.00 N HETATM 5 N3 GF0 A 1 32.899 26.872 25.727 1.00 0.00 N HETATM 6 C4 GF0 A 1 33.431 25.820 25.038 1.00 0.00 C HETATM 7 C5 GF0 A 1 34.040 25.872 23.805 1.00 0.00 C HETATM 8 C6 GF0 A 1 34.163 27.145 23.155 1.00 0.00 C HETATM 9 O6 GF0 A 1 34.707 27.396 22.082 1.00 0.00 O HETATM 10 N7 GF0 A 1 34.485 24.604 23.425 1.00 0.00 N HETATM 11 C8 GF0 A 1 34.146 23.841 24.428 1.00 0.00 C HETATM 12 N9 GF0 A 1 33.502 24.506 25.451 1.00 0.00 N HETATM 13 C1' GF0 A 1 33.124 23.995 26.796 1.00 0.00 C HETATM 14 C2' GF0 A 1 31.615 24.075 27.075 1.00 0.00 C HETATM 15 C3' GF0 A 1 31.128 22.755 26.473 1.00 0.00 C HETATM 16 O3' GF0 A 1 29.927 22.287 27.069 1.00 0.00 O HETATM 17 C4' GF0 A 1 32.306 21.816 26.772 1.00 0.00 C HETATM 18 O4' GF0 A 1 33.480 22.617 26.874 1.00 0.00 O HETATM 19 C5' GF0 A 1 32.504 20.728 25.703 1.00 0.00 C HETATM 20 O5' GF0 A 1 31.394 19.840 25.606 1.00 0.00 O HETATM 21 HN1 GF0 A 1 33.703 29.108 23.469 1.00 0.00 H HETATM 22 HN2 GF0 A 1 32.558 30.006 25.219 1.00 0.00 H HETATM 23 HN2A GF0 A 1 32.073 28.977 26.552 1.00 0.00 H HETATM 24 H8 GF0 A 1 34.396 22.785 24.464 1.00 0.00 H HETATM 25 H1' GF0 A 1 33.667 24.572 27.546 1.00 0.00 H HETATM 26 H2' GF0 A 1 31.131 24.936 26.608 1.00 0.00 H HETATM 27 H3' GF0 A 1 31.030 22.882 25.393 1.00 0.00 H HETATM 28 H4' GF0 A 1 32.131 21.338 27.737 1.00 0.00 H HETATM 29 H5'A GF0 A 1 32.671 21.202 24.734 1.00 0.00 H HETATM 30 H5' GF0 A 1 33.397 20.154 25.959 1.00 0.00 H HETATM 31 H5T GF0 A 1 30.606 20.334 25.291 1.00 0.00 H