HEADER DNA 28-JUL-20 7JKU TITLE CRYSTAL STRUCTURE OF A FOUR-TETRAD, PARALLEL, AND K+ STABILIZED TITLE 2 TETRAHYMENA THERMOPHILA TELOMERIC G-QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 26-MER DNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES 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 L.A.YATSUNYK,S.E.MCCARTHY,D.BESEISO,E.P.GALLAGHER,E.V.CHEN,J.MIAO REVDAT 3 03-APR-24 7JKU 1 REMARK REVDAT 2 28-DEC-22 7JKU 1 JRNL REVDAT 1 07-JUL-21 7JKU 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. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18_3845 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 5285 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.930 REMARK 3 FREE R VALUE TEST SET COUNT : 525 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 32.6000 - 3.1300 0.97 1293 142 0.2126 0.2333 REMARK 3 2 3.1300 - 2.4800 0.97 1216 132 0.3199 0.3064 REMARK 3 3 2.4800 - 2.1700 0.97 1202 134 0.3131 0.3271 REMARK 3 4 2.1700 - 1.9700 0.85 1049 117 0.4254 0.4581 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 46.903 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.16 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 : 0.006 589 REMARK 3 ANGLE : 0.756 913 REMARK 3 CHIRALITY : 0.038 100 REMARK 3 PLANARITY : 0.004 23 REMARK 3 DIHEDRAL : 36.765 253 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): -4.1411 -16.0484 6.6327 REMARK 3 T TENSOR REMARK 3 T11: 0.4664 T22: 0.3517 REMARK 3 T33: 0.4604 T12: -0.0220 REMARK 3 T13: 0.0319 T23: -0.0284 REMARK 3 L TENSOR REMARK 3 L11: 7.2401 L22: 5.3757 REMARK 3 L33: 7.1548 L12: 0.2919 REMARK 3 L13: 0.9556 L23: -0.9092 REMARK 3 S TENSOR REMARK 3 S11: -0.0515 S12: -0.5156 S13: 0.5313 REMARK 3 S21: 0.5748 S22: 0.1045 S23: -0.0080 REMARK 3 S31: -0.1248 S32: 0.1280 S33: -0.0691 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 7JKU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250949. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAY-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) : 0.97918 REMARK 200 MONOCHROMATOR : NULL 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 : 5471 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 59.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 1.18.2_3874 REMARK 200 STARTING MODEL: TEL26-1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, KCL, PEG, NACL, REMARK 280 ETHYLENE GLYCOL, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.55500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.51000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.55500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.51000 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 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 101 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DT A 8 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT A 8 C7 C6 REMARK 470 DT A 15 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT A 15 C7 C6 REMARK 470 DT A 20 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT A 20 C7 C6 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 4 O6 REMARK 620 2 DG A 4 O6 0.0 REMARK 620 3 DG A 10 O6 68.9 68.9 REMARK 620 4 DG A 10 O6 68.9 68.9 0.0 REMARK 620 5 DG A 16 O6 107.7 107.7 68.5 68.5 REMARK 620 6 DG A 16 O6 107.7 107.7 68.5 68.5 0.0 REMARK 620 7 DG A 22 O6 67.4 67.4 106.3 106.3 72.4 72.4 REMARK 620 8 DG A 22 O6 67.4 67.4 106.3 106.3 72.4 72.4 0.0 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 4 O6 REMARK 620 2 DG A 5 O6 83.6 REMARK 620 3 DG A 10 O6 73.3 100.2 REMARK 620 4 DG A 11 O6 143.7 72.8 84.0 REMARK 620 5 DG A 16 O6 107.9 158.4 67.2 88.0 REMARK 620 6 DG A 17 O6 146.4 102.4 135.9 67.5 78.5 REMARK 620 7 DG A 22 O6 68.3 133.9 105.3 146.9 67.7 85.1 REMARK 620 8 DG A 23 O6 88.6 63.4 157.3 104.2 133.2 65.9 79.6 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 5 O6 REMARK 620 2 DG A 6 O6 74.1 REMARK 620 3 DG A 11 O6 74.1 94.7 REMARK 620 4 DG A 12 O6 128.3 73.8 69.4 REMARK 620 5 DG A 17 O6 103.7 163.5 69.3 96.3 REMARK 620 6 DG A 18 O6 153.0 118.3 124.8 78.6 71.1 REMARK 620 7 DG A 23 O6 62.6 124.4 104.6 161.8 65.7 92.1 REMARK 620 8 DG A 24 O6 88.8 72.3 161.0 117.9 124.1 74.1 73.5 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 6 O6 REMARK 620 2 DG A 7 O6 72.3 REMARK 620 3 DG A 12 O6 67.0 87.1 REMARK 620 4 DG A 13 O6 125.9 71.0 72.9 REMARK 620 5 DG A 18 O6 102.4 157.6 71.0 97.0 REMARK 620 6 DG A 19 O6 159.0 120.3 126.8 75.1 72.2 REMARK 620 7 DG A 24 O6 65.7 125.9 105.2 163.1 67.0 94.0 REMARK 620 8 DG A 25 O6 88.0 75.4 153.1 118.6 126.7 80.0 70.8 REMARK 620 9 HOH A 203 O 123.2 58.5 130.7 63.5 133.8 62.7 123.2 55.2 REMARK 620 N 1 2 3 4 5 6 7 8 DBREF 7JKU A 1 26 PDB 7JKU 7JKU 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 K A 104 1 HETNAM K POTASSIUM ION FORMUL 2 K 4(K 1+) FORMUL 6 HOH *9(H2 O) LINK O6 DG A 4 K K A 101 1555 1555 2.80 LINK O6 DG A 4 K K A 101 1555 2545 2.80 LINK O6 DG A 4 K K A 102 1555 1555 2.60 LINK O6 DG A 5 K K A 102 1555 1555 2.65 LINK O6 DG A 5 K K A 103 1555 1555 2.65 LINK O6 DG A 6 K K A 103 1555 1555 2.65 LINK O6 DG A 6 K K A 104 1555 1555 2.91 LINK O6 DG A 7 K K A 104 1555 1555 2.66 LINK O6 DG A 10 K K A 101 1555 1555 2.74 LINK O6 DG A 10 K K A 101 1555 2545 2.74 LINK O6 DG A 10 K K A 102 1555 1555 2.64 LINK O6 DG A 11 K K A 102 1555 1555 2.76 LINK O6 DG A 11 K K A 103 1555 1555 2.68 LINK O6 DG A 12 K K A 103 1555 1555 2.71 LINK O6 DG A 12 K K A 104 1555 1555 2.91 LINK O6 DG A 13 K K A 104 1555 1555 2.60 LINK O6 DG A 16 K K A 101 1555 1555 2.70 LINK O6 DG A 16 K K A 101 1555 2545 2.70 LINK O6 DG A 16 K K A 102 1555 1555 2.88 LINK O6 DG A 17 K K A 102 1555 1555 2.78 LINK O6 DG A 17 K K A 103 1555 1555 2.73 LINK O6 DG A 18 K K A 103 1555 1555 2.65 LINK O6 DG A 18 K K A 104 1555 1555 2.92 LINK O6 DG A 19 K K A 104 1555 1555 2.64 LINK O6 DG A 22 K K A 101 1555 1555 2.61 LINK O6 DG A 22 K K A 101 1555 2545 2.61 LINK O6 DG A 22 K K A 102 1555 1555 2.74 LINK O6 DG A 23 K K A 102 1555 1555 2.71 LINK O6 DG A 23 K K A 103 1555 1555 2.77 LINK O6 DG A 24 K K A 103 1555 1555 2.73 LINK O6 DG A 24 K K A 104 1555 1555 2.95 LINK O6 DG A 25 K K A 104 1555 1555 2.65 LINK K K A 104 O HOH A 203 1555 1555 3.19 CRYST1 32.042 39.110 59.020 90.00 90.00 90.00 P 2 21 21 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 0.031209 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025569 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016943 0.00000