HEADER DNA 23-MAR-20 6W9P TITLE TEL26 PARALLEL FOUR-QUARTET G-QUADRUPLEX WITH K+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(P*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP COMPND 4 *GP*GP*GP*T)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: DT26 HAS NO BASE AND ONLY THE PHOSPHATE IS MODELED. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: TETRAHYMENA THERMOPHILA; SOURCE 4 ORGANISM_TAXID: 5911 KEYWDS G-QUADRUPLEX, PARALLEL, FOUR-QUARTETS, PROPELLER LOOPS, DNA EXPDTA X-RAY DIFFRACTION AUTHOR S.E.MCCARTHY,L.A.YATSUNYK,D.BESEISO,J.MIAO REVDAT 3 18-OCT-23 6W9P 1 REMARK REVDAT 2 13-APR-22 6W9P 1 JRNL REVDAT 1 31-MAR-21 6W9P 0 JRNL AUTH D.BESEISO,E.V.CHEN,S.E.MCCARTHY,K.N.MARTIN,E.P.GALLAGHER, JRNL AUTH 2 J.MIAO,L.A.YATSUNYK JRNL TITL THE FIRST CRYSTAL STRUCTURES OF HYBRID AND PARALLEL JRNL TITL 2 FOUR-TETRAD INTRAMOLECULAR G-QUADRUPLEXES. JRNL REF NUCLEIC ACIDS RES. V. 50 2959 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 35212369 JRNL DOI 10.1093/NAR/GKAC091 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 4078 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.830 REMARK 3 FREE R VALUE TEST SET COUNT : 401 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 33.5000 - 2.8700 0.99 1289 142 0.1694 0.1748 REMARK 3 2 2.8700 - 2.2800 1.00 1213 125 0.2614 0.3029 REMARK 3 3 2.2800 - 1.9900 0.97 1175 134 0.2712 0.3365 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) : 0.234 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.504 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.94 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 : 0.005 619 REMARK 3 ANGLE : 0.722 961 REMARK 3 CHIRALITY : 0.036 103 REMARK 3 PLANARITY : 0.005 26 REMARK 3 DIHEDRAL : 34.657 256 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): -10.6721 6.7064 6.0994 REMARK 3 T TENSOR REMARK 3 T11: 0.2773 T22: 0.2304 REMARK 3 T33: 0.3496 T12: -0.0386 REMARK 3 T13: -0.0290 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 4.7352 L22: 3.9951 REMARK 3 L33: 4.2361 L12: -0.1951 REMARK 3 L13: -1.0946 L23: 0.9459 REMARK 3 S TENSOR REMARK 3 S11: -0.1037 S12: 0.0531 S13: 0.0650 REMARK 3 S21: -0.2871 S22: -0.0400 S23: -0.0467 REMARK 3 S31: -0.4820 S32: -0.0937 S33: 0.1731 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 6W9P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247768. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 196 REMARK 200 PH : 6.5 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-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : CRYOGENICALLY-COOLED SINGLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4116 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 64.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.87500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1O0K REMARK 200 REMARK 200 REMARK: RELATIVELY THINK SHEETS, LOOK CLAM-SHELL SHAPED. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32% PEG 2000, 0.3M SODIUM CHLORIDE, REMARK 280 0.05M SODIUM CACODYLATE PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.64033 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.28067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.28067 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.64033 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 NA A 104 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 3 O2 REMARK 620 2 DG A 17 OP1 117.8 REMARK 620 3 HOH A 213 O 121.4 3.9 REMARK 620 4 HOH A 221 O 126.7 11.3 10.0 REMARK 620 5 HOH A 224 O 108.5 10.8 14.7 18.3 REMARK 620 6 HOH A 229 O 118.2 13.3 15.0 10.2 12.7 REMARK 620 N 1 2 3 4 5 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 4 O6 REMARK 620 2 DG A 5 O6 73.0 REMARK 620 3 DG A 10 O6 79.5 89.2 REMARK 620 4 DG A 11 O6 136.7 68.6 80.6 REMARK 620 5 DG A 16 O6 128.1 151.2 77.8 83.8 REMARK 620 6 DG A 17 O6 140.0 94.6 139.4 63.6 79.8 REMARK 620 7 DG A 22 O6 81.7 123.7 134.6 137.1 82.2 74.1 REMARK 620 8 DG A 23 O6 82.5 60.0 147.8 94.9 133.7 59.1 67.6 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 5 O6 REMARK 620 2 DG A 6 O6 74.4 REMARK 620 3 DG A 11 O6 72.2 95.1 REMARK 620 4 DG A 12 O6 133.3 73.0 78.4 REMARK 620 5 DG A 17 O6 110.8 159.4 69.0 90.6 REMARK 620 6 DG A 18 O6 154.3 107.0 131.9 68.7 77.2 REMARK 620 7 DG A 23 O6 72.7 127.2 112.4 153.6 72.5 87.4 REMARK 620 8 DG A 24 O6 94.3 68.9 161.7 104.0 128.6 63.9 73.6 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 6 O6 REMARK 620 2 DG A 7 O6 74.5 REMARK 620 3 DG A 12 O6 67.5 86.7 REMARK 620 4 DG A 13 O6 129.9 74.3 72.5 REMARK 620 5 DG A 18 O6 101.7 155.4 69.8 91.2 REMARK 620 6 DG A 19 O6 155.8 122.0 126.5 74.0 70.6 REMARK 620 7 DG A 24 O6 65.7 129.0 105.1 156.7 66.8 90.5 REMARK 620 8 DG A 25 O6 93.1 78.6 158.3 117.7 126.0 75.1 73.3 REMARK 620 N 1 2 3 4 5 6 7 DBREF 6W9P A 1 26 PDB 6W9P 6W9P 1 26 SEQRES 1 A 26 DG DT DT DG DG DG DG DT DT DG DG DG DG SEQRES 2 A 26 DT DT DG DG DG DG DT DT DG DG DG DG DT HET K A 101 1 HET K A 102 1 HET K A 103 1 HET NA A 104 1 HETNAM K POTASSIUM ION HETNAM NA SODIUM ION FORMUL 2 K 3(K 1+) FORMUL 5 NA NA 1+ FORMUL 6 HOH *30(H2 O) LINK O2 DT A 3 NA NA A 104 1555 6555 2.64 LINK O6 DG A 4 K K A 101 1555 1555 2.67 LINK O6 DG A 5 K K A 101 1555 1555 2.92 LINK O6 DG A 5 K K A 102 1555 1555 2.66 LINK O6 DG A 6 K K A 102 1555 1555 2.69 LINK O6 DG A 6 K K A 103 1555 1555 3.02 LINK O6 DG A 7 K K A 103 1555 1555 2.64 LINK O6 DG A 10 K K A 101 1555 1555 2.62 LINK O6 DG A 11 K K A 101 1555 1555 2.74 LINK O6 DG A 11 K K A 102 1555 1555 2.76 LINK O6 DG A 12 K K A 102 1555 1555 2.81 LINK O6 DG A 12 K K A 103 1555 1555 2.86 LINK O6 DG A 13 K K A 103 1555 1555 2.78 LINK O6 DG A 16 K K A 101 1555 1555 2.48 LINK O6 DG A 17 K K A 101 1555 1555 3.17 LINK O6 DG A 17 K K A 102 1555 1555 2.78 LINK OP1 DG A 17 NA NA A 104 1555 1555 2.56 LINK O6 DG A 18 K K A 102 1555 1555 2.88 LINK O6 DG A 18 K K A 103 1555 1555 2.75 LINK O6 DG A 19 K K A 103 1555 1555 2.73 LINK O6 DG A 22 K K A 101 1555 1555 2.47 LINK O6 DG A 23 K K A 101 1555 1555 3.41 LINK O6 DG A 23 K K A 102 1555 1555 2.72 LINK O6 DG A 24 K K A 102 1555 1555 2.90 LINK O6 DG A 24 K K A 103 1555 1555 2.80 LINK O6 DG A 25 K K A 103 1555 1555 2.63 LINK NA NA A 104 O HOH A 213 1555 1555 2.36 LINK NA NA A 104 O HOH A 221 1555 1555 2.36 LINK NA NA A 104 O HOH A 224 1555 1555 2.74 LINK NA NA A 104 O HOH A 229 1555 1555 2.51 CRYST1 38.681 38.681 64.921 90.00 90.00 120.00 P 31 2 1 6 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 0.025852 0.014926 0.000000 0.00000 SCALE2 0.000000 0.029852 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015403 0.00000