HEADER DNA 25-MAY-23 8P6B TITLE RUTHENIUM COMPLEX BOUND TO AN ANTIPARALLEL G-QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: UNIMOLECULAR DNA G-QUADRUPLEX SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS G-QUADRUPLEX, ANTIPARALLEL, RUTHENIUM POLYPYRIDYL, SYN-GUANOSINE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR K.T.MCQUAID,C.J.CARDIN REVDAT 1 12-JUN-24 8P6B 0 JRNL AUTH K.T.MCQUAID,C.J.CARDIN JRNL TITL RUTHENIUM COMPLEX BOUND TO AN ANTIPARALLEL G-QUADRUPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 4498 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.260 REMARK 3 R VALUE (WORKING SET) : 0.259 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.340 REMARK 3 FREE R VALUE TEST SET COUNT : 240 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 25.2300 - 3.1500 0.96 2170 107 0.2429 0.2594 REMARK 3 2 3.1500 - 2.5000 0.95 2088 133 0.3555 0.3426 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.005 572 REMARK 3 ANGLE : 0.758 898 REMARK 3 CHIRALITY : 0.036 82 REMARK 3 PLANARITY : 0.004 24 REMARK 3 DIHEDRAL : 35.887 203 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 5 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.6122 1.9459 -31.2444 REMARK 3 T TENSOR REMARK 3 T11: 1.3215 T22: 1.7104 REMARK 3 T33: 1.1219 T12: 0.1593 REMARK 3 T13: 0.0200 T23: -0.0302 REMARK 3 L TENSOR REMARK 3 L11: 2.2598 L22: 3.4526 REMARK 3 L33: 6.4403 L12: 2.6036 REMARK 3 L13: -2.7780 L23: -4.5294 REMARK 3 S TENSOR REMARK 3 S11: 1.4927 S12: -2.3943 S13: 1.4889 REMARK 3 S21: 2.1546 S22: 0.1115 S23: -1.1540 REMARK 3 S31: -2.1457 S32: 1.6520 S33: 0.2190 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 6 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.1086 2.4225 -37.4283 REMARK 3 T TENSOR REMARK 3 T11: 1.2522 T22: 0.9160 REMARK 3 T33: 0.8842 T12: 0.1053 REMARK 3 T13: 0.1153 T23: 0.0262 REMARK 3 L TENSOR REMARK 3 L11: 0.0896 L22: 0.0472 REMARK 3 L33: 1.9245 L12: -0.1885 REMARK 3 L13: -0.6818 L23: -0.1897 REMARK 3 S TENSOR REMARK 3 S11: 0.3562 S12: 0.0050 S13: 0.6903 REMARK 3 S21: 1.7259 S22: 0.4028 S23: 1.3415 REMARK 3 S31: -1.7782 S32: -1.1236 S33: 0.0104 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 21 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.0408 -7.7086 -33.5977 REMARK 3 T TENSOR REMARK 3 T11: 0.9234 T22: 0.8229 REMARK 3 T33: 0.7242 T12: 0.2354 REMARK 3 T13: -0.0911 T23: 0.1564 REMARK 3 L TENSOR REMARK 3 L11: 3.2204 L22: 4.2528 REMARK 3 L33: 3.9075 L12: -0.3968 REMARK 3 L13: 2.5905 L23: -0.0015 REMARK 3 S TENSOR REMARK 3 S11: -0.1197 S12: 1.0305 S13: 0.7567 REMARK 3 S21: 0.1652 S22: 0.1111 S23: -1.8262 REMARK 3 S31: 0.3806 S32: 1.3778 S33: 0.5543 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 8P6B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292130759. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.5585 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6187 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 47.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 37.30 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 FOR SHELL : 0.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M POTASSIUM CHLORIDE, 0.04 M REMARK 280 SODIUM CHLORIDE, 0.02 M SODIUM CACODYLATE TRIHYDRATE PH 5.5, REMARK 280 17.5% V/V MPD, 0.001 M HEXAMINE COBALT(III) CHLORIDE, AND 0.01 M REMARK 280 MAGNESIUM CHLORIDE HEXAHYDRATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 95.52933 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 47.76467 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 47.76467 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 95.52933 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 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 DG A 1 O5' C5' 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 103 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 O6 REMARK 620 2 DG A 2 O6 61.6 REMARK 620 3 DG A 8 O6 129.8 94.4 REMARK 620 4 DG A 9 O6 78.1 114.0 73.0 REMARK 620 5 DG A 13 O6 118.9 164.8 95.5 80.0 REMARK 620 6 DG A 14 O6 162.5 101.0 48.1 113.0 77.4 REMARK 620 7 DG A 20 O6 108.4 63.5 95.7 168.4 104.0 58.4 REMARK 620 8 DG A 21 O6 75.4 102.0 154.7 116.2 65.0 109.1 75.0 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 2 O6 REMARK 620 2 DG A 3 O6 69.4 REMARK 620 3 DG A 7 O6 124.7 77.4 REMARK 620 4 DG A 8 O6 101.5 133.9 71.8 REMARK 620 5 DG A 14 O6 109.3 176.2 106.0 49.6 REMARK 620 6 DG A 15 O6 154.2 107.9 77.4 98.0 71.6 REMARK 620 7 DG A 19 O6 88.8 64.7 115.3 161.0 112.0 68.1 REMARK 620 8 DG A 20 O6 68.5 115.4 165.4 101.0 61.0 91.4 67.7 REMARK 620 N 1 2 3 4 5 6 7 DBREF 8P6B A 1 21 PDB 8P6B 8P6B 1 21 SEQRES 1 A 21 DG DG DG DT DT DT DG DG DG DT DT DA DG SEQRES 2 A 21 DG DG DT DT DA DG DG DG HET 0K8 A 101 89 HET K A 102 1 HET K A 103 1 HETNAM 0K8 RUTHENIUM BIS-(PHENANTHROLINE) 12,17-DIHYDRO- HETNAM 2 0K8 NAPHTHODIPYRIDOPHENAZINE-12,17-DIONE HETNAM K POTASSIUM ION HETSYN 0K8 RUTHENIUM POLYPRIDYL COMPLEX FORMUL 2 0K8 C50 H28 N8 O2 RU 2+ FORMUL 3 K 2(K 1+) LINK O6 DG A 1 K K A 103 1555 1555 2.63 LINK O6 DG A 2 K K A 102 1555 1555 2.98 LINK O6 DG A 2 K K A 103 1555 1555 3.22 LINK O6 DG A 3 K K A 102 1555 1555 3.19 LINK O6 DG A 7 K K A 102 1555 1555 2.68 LINK O6 DG A 8 K K A 102 1555 1555 3.03 LINK O6 DG A 8 K K A 103 1555 1555 3.12 LINK O6 DG A 9 K K A 103 1555 1555 2.72 LINK O6 DG A 13 K K A 103 1555 1555 2.56 LINK O6 DG A 14 K K A 102 1555 1555 2.69 LINK O6 DG A 14 K K A 103 1555 1555 2.76 LINK O6 DG A 15 K K A 102 1555 1555 2.99 LINK O6 DG A 19 K K A 102 1555 1555 2.70 LINK O6 DG A 20 K K A 102 1555 1555 2.66 LINK O6 DG A 20 K K A 103 1555 1555 2.81 LINK O6 DG A 21 K K A 103 1555 1555 2.84 CRYST1 29.131 29.131 143.294 90.00 90.00 120.00 P 32 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 0.034327 0.019819 0.000000 0.00000 SCALE2 0.000000 0.039638 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006979 0.00000