HEADER DNA 27-JUN-23 8TAA TITLE RIGHT-LEFT HYBRID PARALLEL G-QUADRUPLEX IN COMPLEX WITH N-METHYL TITLE 2 MESOPORPHYRIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (25-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, RIGHT-LEFT-HANDED, PARALLEL, NMM, DNA EXPDTA X-RAY DIFFRACTION AUTHOR P.C.SETH,L.A.YATSUNYK REVDAT 4 05-FEB-25 8TAA 1 JRNL REVDAT 3 15-JAN-25 8TAA 1 JRNL REVDAT 2 16-OCT-24 8TAA 1 COMPND REMARK HET HETNAM REVDAT 2 2 1 FORMUL LINK ATOM REVDAT 1 03-JUL-24 8TAA 0 JRNL AUTH P.SETH,E.XING,A.D.HENDRICKSON,K.LI,R.MONSEN,J.B.CHAIRES, JRNL AUTH 2 S.NEIDLE,L.A.YATSUNYK JRNL TITL INTERACTION OF N-METHYLMESOPORPHYRIN IX WITH A HYBRID JRNL TITL 2 LEFT-/RIGHT-HANDED G-QUADRUPLEX MOTIF FROM THE PROMOTER OF JRNL TITL 3 THE SLC2A1 GENE. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 39704129 JRNL DOI 10.1093/NAR/GKAE1208 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13049 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.380 REMARK 3 FREE R VALUE TEST SET COUNT : 702 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 35.3900 - 2.4800 1.00 2654 154 0.1608 0.2046 REMARK 3 2 2.4800 - 1.9700 1.00 2471 142 0.2368 0.2649 REMARK 3 3 1.9700 - 1.7200 1.00 2408 137 0.1893 0.2937 REMARK 3 4 1.7200 - 1.5600 1.00 2414 127 0.1789 0.2283 REMARK 3 5 1.5600 - 1.4500 1.00 2400 142 0.2387 0.3081 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.336 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 752 REMARK 3 ANGLE : 1.009 1162 REMARK 3 CHIRALITY : 0.041 116 REMARK 3 PLANARITY : 0.010 33 REMARK 3 DIHEDRAL : 34.908 331 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8TAA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1000274691. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 196 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13141 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 141.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.78900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.21.2_5419 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: AMORPHOUS CUBES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 MM SPERMINE, 45% MPD, 0.08 M NACL, REMARK 280 0.04 M NACACO PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.77150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 15.44850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 15.44850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.38575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 15.44850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 15.44850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 106.15725 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 15.44850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 15.44850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.38575 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 15.44850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 15.44850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 106.15725 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 70.77150 REMARK 290 REMARK 290 REMARK: NULL 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 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 MMP A 103 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 104 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 O6 REMARK 620 2 DG A 3 O6 91.0 REMARK 620 3 DG A 4 O6 66.5 79.6 REMARK 620 4 DG A 6 O6 157.1 73.4 93.7 REMARK 620 5 DG A 7 O6 102.5 133.4 66.2 78.0 REMARK 620 6 DG A 9 O6 133.3 109.4 156.1 69.0 93.3 REMARK 620 7 DG A 10 O6 67.1 155.0 100.9 131.0 66.4 80.3 REMARK 620 8 DG A 12 O6 75.7 68.8 129.7 112.4 157.7 73.7 93.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 105 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 O6 REMARK 620 2 DG A 4 O6 69.5 REMARK 620 3 DG A 7 O6 107.4 69.4 REMARK 620 4 DG A 10 O6 69.0 105.9 68.5 REMARK 620 5 DG A 15 O6 87.6 150.6 137.5 81.2 REMARK 620 6 DG A 18 O6 149.6 139.8 83.6 90.1 66.9 REMARK 620 7 DG A 21 O6 136.8 83.8 93.2 153.5 102.6 68.1 REMARK 620 8 DG A 21 O6 136.9 79.1 87.4 150.7 108.8 70.2 6.4 REMARK 620 9 DG A 24 O6 80.0 88.9 151.7 137.4 68.6 104.0 65.8 70.4 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 106 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 15 O6 REMARK 620 2 DG A 16 O6 74.6 REMARK 620 3 DG A 18 O6 66.7 89.5 REMARK 620 4 DG A 19 O6 132.2 75.3 76.8 REMARK 620 5 DG A 21 O6 106.0 157.0 70.4 88.8 REMARK 620 6 DG A 21 O6 102.2 155.0 67.1 90.3 4.1 REMARK 620 7 DG A 22 O6 152.7 115.2 135.2 74.7 75.1 79.2 REMARK 620 8 DG A 24 O6 67.7 130.7 103.0 153.8 67.2 66.5 88.7 REMARK 620 9 DG A 24 O6 71.8 131.1 108.1 152.2 68.3 68.0 84.0 5.3 REMARK 620 N 1 2 3 4 5 6 7 8 DBREF 8TAA A 1 25 PDB 8TAA 8TAA 1 25 SEQRES 1 A 25 DG DT DG DG DT DG DG DT DG DG DT DG DA SEQRES 2 A 25 DT DG DG DT DG DG DT DG DG DT DG DG HET SPK A 101 14 HET MPD A 102 8 HET MMP A 103 36 HET K A 104 1 HET K A 105 1 HET K A 106 1 HETNAM SPK SPERMINE (FULLY PROTONATED FORM) HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM MMP N-METHYLMESOPORPHYRIN HETNAM K POTASSIUM ION FORMUL 2 SPK C10 H30 N4 4+ FORMUL 3 MPD C6 H14 O2 FORMUL 4 MMP C35 H40 N4 O4 FORMUL 5 K 3(K 1+) FORMUL 8 HOH *62(H2 O) LINK O6 DG A 1 K K A 104 1555 1555 2.89 LINK O6 DG A 1 K K A 105 1555 1555 2.80 LINK O6 DG A 3 K K A 104 1555 1555 2.74 LINK O6 DG A 4 K K A 104 1555 1555 2.90 LINK O6 DG A 4 K K A 105 1555 1555 2.76 LINK O6 DG A 6 K K A 104 1555 1555 2.81 LINK O6 DG A 7 K K A 104 1555 1555 2.93 LINK O6 DG A 7 K K A 105 1555 1555 2.83 LINK O6 DG A 9 K K A 104 1555 1555 2.79 LINK O6 DG A 10 K K A 104 1555 1555 2.83 LINK O6 DG A 10 K K A 105 1555 1555 2.78 LINK O6 DG A 12 K K A 104 1555 1555 2.79 LINK O6 DG A 15 K K A 105 1555 1555 2.87 LINK O6 DG A 15 K K A 106 1555 1555 2.88 LINK O6 DG A 16 K K A 106 1555 1555 2.70 LINK O6 DG A 18 K K A 105 1555 1555 2.84 LINK O6 DG A 18 K K A 106 1555 1555 2.83 LINK O6 DG A 19 K K A 106 1555 1555 2.71 LINK O6 A DG A 21 K K A 105 1555 1555 2.90 LINK O6 B DG A 21 K K A 105 1555 1555 2.78 LINK O6 A DG A 21 K K A 106 1555 1555 2.74 LINK O6 B DG A 21 K K A 106 1555 1555 3.01 LINK O6 DG A 22 K K A 106 1555 1555 2.67 LINK O6 A DG A 24 K K A 105 1555 1555 2.79 LINK O6 B DG A 24 K K A 105 1555 1555 3.01 LINK O6 A DG A 24 K K A 106 1555 1555 2.84 LINK O6 B DG A 24 K K A 106 1555 1555 2.76 LINK O6 DG A 25 K K A 106 1555 1555 2.76 CRYST1 30.897 30.897 141.543 90.00 90.00 90.00 P 41 21 2 8 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 0.032366 0.000000 0.000000 0.00000 SCALE2 0.000000 0.032366 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007065 0.00000 CONECT 14 674 675 CONECT 56 674 CONECT 78 674 675 CONECT 120 674 CONECT 142 674 675 CONECT 184 674 CONECT 206 674 675 CONECT 248 674 CONECT 311 675 676 CONECT 333 676 CONECT 375 675 676 CONECT 397 676 CONECT 475 675 676 CONECT 476 675 676 CONECT 503 676 CONECT 581 675 676 CONECT 582 675 676 CONECT 609 676 CONECT 616 617 CONECT 617 616 618 CONECT 618 617 619 CONECT 619 618 620 CONECT 620 619 621 CONECT 621 620 622 CONECT 622 621 623 CONECT 623 622 624 CONECT 624 623 625 CONECT 625 624 626 CONECT 626 625 627 CONECT 627 626 628 CONECT 628 627 629 CONECT 629 628 CONECT 630 631 CONECT 631 630 632 633 634 CONECT 632 631 CONECT 633 631 CONECT 634 631 635 CONECT 635 634 636 637 CONECT 636 635 CONECT 637 635 CONECT 638 639 CONECT 639 638 640 643 CONECT 640 639 641 670 CONECT 641 640 642 645 CONECT 642 641 643 646 CONECT 643 639 642 644 CONECT 644 643 649 CONECT 645 641 CONECT 646 642 647 CONECT 647 646 CONECT 648 649 652 CONECT 649 644 648 650 CONECT 650 649 651 654 CONECT 651 650 652 655 CONECT 652 648 651 653 CONECT 653 652 657 CONECT 654 650 CONECT 655 651 CONECT 656 657 660 CONECT 657 653 656 658 CONECT 658 657 659 662 CONECT 659 658 660 663 CONECT 660 656 659 661 CONECT 661 660 666 CONECT 662 658 CONECT 663 659 664 CONECT 664 663 CONECT 665 666 669 CONECT 666 661 665 667 CONECT 667 666 668 672 CONECT 668 667 669 671 CONECT 669 665 668 670 CONECT 670 640 669 CONECT 671 668 CONECT 672 667 673 CONECT 673 672 CONECT 674 14 56 78 120 CONECT 674 142 184 206 248 CONECT 675 14 78 142 206 CONECT 675 311 375 475 476 CONECT 675 581 582 CONECT 676 311 333 375 397 CONECT 676 475 476 503 581 CONECT 676 582 609 MASTER 260 0 6 0 0 0 0 6 653 1 84 2 END