HEADER DNA 03-JUN-24 9C46 TITLE RIGHT-LEFT HYBRID PARALLEL G-QUADRUPLEX FROM SLC2A1 PROMOTER 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, DNA EXPDTA X-RAY DIFFRACTION AUTHOR E.R.XING,L.A.YATSUNYK REVDAT 2 05-FEB-25 9C46 1 JRNL REVDAT 1 15-JAN-25 9C46 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. 2.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 2425 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.690 REMARK 3 FREE R VALUE TEST SET COUNT : 138 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 25.1000 - 2.3900 0.97 2287 138 0.2334 0.2543 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.286 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.127 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.36 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 : 0.004 603 REMARK 3 ANGLE : 0.668 935 REMARK 3 CHIRALITY : 0.038 100 REMARK 3 PLANARITY : 0.004 25 REMARK 3 DIHEDRAL : 37.575 247 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -7.3723 -15.0395 0.6118 REMARK 3 T TENSOR REMARK 3 T11: 0.2284 T22: 0.9001 REMARK 3 T33: 0.3409 T12: -0.0521 REMARK 3 T13: 0.0471 T23: 0.0155 REMARK 3 L TENSOR REMARK 3 L11: 1.2325 L22: 1.3975 REMARK 3 L33: 8.1672 L12: -1.2825 REMARK 3 L13: 0.0401 L23: -0.5661 REMARK 3 S TENSOR REMARK 3 S11: -0.0477 S12: -0.1041 S13: -0.3287 REMARK 3 S21: 0.0086 S22: 0.3507 S23: 0.9939 REMARK 3 S31: 0.8235 S32: -3.1723 S33: 0.5126 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 9C46 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1000284672. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-23 REMARK 200 TEMPERATURE (KELVIN) : 196 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.920105 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2469 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.388 REMARK 200 RESOLUTION RANGE LOW (A) : 30.523 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 1.38300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.19.2_4158 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: LONG NEEDLES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08 M NACL 0.04 M NA CACODYLATE PH REMARK 280 6.0 45% MPD, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 32.06850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.74550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.06850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.74550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 K K A 104 LIES ON A SPECIAL POSITION. 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 101 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 60.8 73.0 REMARK 620 4 DG A 6 O6 145.0 64.8 87.1 REMARK 620 5 DG A 7 O6 101.4 133.1 74.4 80.9 REMARK 620 6 DG A 9 O6 141.7 107.8 156.0 72.5 89.7 REMARK 620 7 DG A 10 O6 68.4 158.8 100.0 135.9 60.0 86.8 REMARK 620 8 DG A 12 O6 78.1 68.5 122.0 112.1 158.2 78.5 100.8 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 102 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 O6 REMARK 620 2 DG A 4 O6 65.3 REMARK 620 3 DG A 7 O6 106.3 74.2 REMARK 620 4 DG A 10 O6 78.3 110.6 62.0 REMARK 620 5 DG A 15 O6 96.9 151.7 133.7 85.0 REMARK 620 6 DG A 18 O6 154.9 139.7 83.5 86.6 61.5 REMARK 620 7 DG A 21 O6 137.1 82.5 90.2 142.3 99.5 64.1 REMARK 620 8 DG A 24 O6 82.3 86.2 152.1 145.4 69.1 99.9 67.3 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 103 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 15 O6 REMARK 620 2 DG A 16 O6 80.4 REMARK 620 3 DG A 18 O6 66.0 85.5 REMARK 620 4 DG A 19 O6 127.5 60.0 77.1 REMARK 620 5 DG A 21 O6 106.0 147.8 69.5 93.8 REMARK 620 6 DG A 22 O6 152.5 101.4 141.2 73.9 87.3 REMARK 620 7 DG A 24 O6 72.8 138.5 110.7 158.5 71.7 89.4 REMARK 620 8 DG A 25 O6 92.9 66.9 148.1 100.6 141.9 63.7 83.2 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 104 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 16 O6 REMARK 620 2 DG A 16 O6 0.0 REMARK 620 3 DG A 19 O6 67.3 67.3 REMARK 620 4 DG A 19 O6 67.3 67.3 0.0 REMARK 620 5 DG A 22 O6 106.8 106.8 79.6 79.6 REMARK 620 6 DG A 22 O6 106.8 106.8 79.6 79.6 0.0 REMARK 620 7 DG A 25 O6 73.3 73.3 116.6 116.6 66.7 66.7 REMARK 620 8 DG A 25 O6 73.3 73.3 116.6 116.6 66.7 66.7 0.0 REMARK 620 N 1 2 3 4 5 6 7 DBREF 9C46 A 1 25 PDB 9C46 9C46 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 K A 101 1 HET K A 102 1 HET K A 103 1 HET K A 104 1 HET NA A 105 1 HET MPD A 106 8 HETNAM K POTASSIUM ION HETNAM NA SODIUM ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 K 4(K 1+) FORMUL 6 NA NA 1+ FORMUL 7 MPD C6 H14 O2 FORMUL 8 HOH *(H2 O) LINK O6 DG A 1 K K A 101 1555 1555 3.04 LINK O6 DG A 1 K K A 102 1555 1555 2.73 LINK O6 DG A 3 K K A 101 1555 1555 2.92 LINK O6 DG A 4 K K A 101 1555 1555 3.25 LINK O6 DG A 4 K K A 102 1555 1555 3.15 LINK O6 DG A 6 K K A 101 1555 1555 2.86 LINK O6 DG A 7 K K A 101 1555 1555 2.93 LINK O6 DG A 7 K K A 102 1555 1555 3.05 LINK O6 DG A 9 K K A 101 1555 1555 2.68 LINK O6 DG A 10 K K A 101 1555 1555 2.97 LINK O6 DG A 10 K K A 102 1555 1555 2.63 LINK O6 DG A 12 K K A 101 1555 1555 2.75 LINK O6 DG A 15 K K A 102 1555 1555 2.79 LINK O6 DG A 15 K K A 103 1555 1555 2.69 LINK O6 DG A 16 K K A 103 1555 1555 2.88 LINK O6 DG A 16 K K A 104 1555 1555 2.66 LINK O6 DG A 16 K K A 104 1555 2555 2.65 LINK O6 DG A 18 K K A 102 1555 1555 2.94 LINK O6 DG A 18 K K A 103 1555 1555 2.70 LINK O6 DG A 19 K K A 103 1555 1555 3.06 LINK O6 DG A 19 K K A 104 1555 1555 2.71 LINK O6 DG A 19 K K A 104 1555 2555 2.71 LINK O6 DG A 21 K K A 102 1555 1555 2.80 LINK O6 DG A 21 K K A 103 1555 1555 2.66 LINK O6 DG A 22 K K A 103 1555 1555 2.65 LINK O6 DG A 22 K K A 104 1555 1555 2.67 LINK O6 DG A 22 K K A 104 1555 2555 2.67 LINK O6 DG A 24 K K A 102 1555 1555 2.86 LINK O6 DG A 24 K K A 103 1555 1555 2.71 LINK O6 DG A 25 K K A 103 1555 1555 2.96 LINK O6 DG A 25 K K A 104 1555 1555 2.73 LINK O6 DG A 25 K K A 104 1555 2555 2.72 CRYST1 64.137 31.491 31.500 90.00 104.31 90.00 C 1 2 1 4 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 0.015592 0.000000 0.003977 0.00000 SCALE2 0.000000 0.031755 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032762 0.00000 CONECT 14 532 533 CONECT 56 532 CONECT 78 532 533 CONECT 120 532 CONECT 142 532 533 CONECT 184 532 CONECT 206 532 533 CONECT 248 532 CONECT 311 533 534 CONECT 333 534 535 CONECT 375 533 534 CONECT 397 534 535 CONECT 439 533 534 CONECT 461 534 535 CONECT 503 533 534 CONECT 525 534 535 CONECT 532 14 56 78 120 CONECT 532 142 184 206 248 CONECT 533 14 78 142 206 CONECT 533 311 375 439 503 CONECT 534 311 333 375 397 CONECT 534 439 461 503 525 CONECT 535 333 397 461 525 CONECT 537 538 CONECT 538 537 539 540 541 CONECT 539 538 CONECT 540 538 CONECT 541 538 542 CONECT 542 541 543 544 CONECT 543 542 CONECT 544 542 MASTER 266 0 6 0 0 0 0 6 544 1 31 2 END