HEADER DNA 27-MAR-19 6R6D TITLE [RU(TAP)2(11,12-CN2-DPPZ)]2+ BOUND TO D(TCGGCGCCGA)2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RUTHENIUM, INTERCALATION, DNA, ASYMMETRIC EXPDTA X-RAY DIFFRACTION AUTHOR K.T.MCQUAID,J.P.HALL,C.J.CARDIN REVDAT 5 15-MAY-24 6R6D 1 REMARK REVDAT 4 19-MAY-21 6R6D 1 JRNL REMARK REVDAT 3 11-NOV-20 6R6D 1 LINK REVDAT 2 03-JUN-20 6R6D 1 REMARK REVDAT 1 06-MAY-20 6R6D 0 JRNL AUTH K.MCQUAID,J.P.HALL,J.A.BRAZIER,D.J.CARDIN,C.J.CARDIN JRNL TITL X-RAY CRYSTAL STRUCTURES SHOW DNA STACKING ADVANTAGE OF JRNL TITL 2 TERMINAL NITRILE SUBSTITUTION IN RU-DPPZ COMPLEXES. JRNL REF CHEMISTRY V. 24 15859 2018 JRNL REFN ISSN 0947-6539 JRNL PMID 30063271 JRNL DOI 10.1002/CHEM.201803021 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.15RC2_3433: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 6316 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 310 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 33.0300 - 2.3161 1.00 2993 158 0.1729 0.1666 REMARK 3 2 2.3161 - 1.8384 1.00 3013 152 0.2068 0.3091 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.540 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 : 0.011 294 REMARK 3 ANGLE : 1.150 462 REMARK 3 CHIRALITY : 0.054 42 REMARK 3 PLANARITY : 0.009 13 REMARK 3 DIHEDRAL : 26.202 101 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 1:10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.9589 35.1409 -3.4908 REMARK 3 T TENSOR REMARK 3 T11: 0.3641 T22: 0.3427 REMARK 3 T33: 0.2981 T12: -0.0370 REMARK 3 T13: 0.0479 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 8.8231 L22: 8.4054 REMARK 3 L33: 3.2456 L12: -5.1014 REMARK 3 L13: 2.6968 L23: -5.2352 REMARK 3 S TENSOR REMARK 3 S11: 0.0924 S12: 0.1922 S13: 0.1810 REMARK 3 S21: -0.2833 S22: -0.2389 S23: -0.1213 REMARK 3 S31: 0.2087 S32: 0.0772 S33: 0.2239 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 102:102 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.0715 30.7770 11.1266 REMARK 3 T TENSOR REMARK 3 T11: 0.3713 T22: 0.4929 REMARK 3 T33: 0.3176 T12: -0.0210 REMARK 3 T13: 0.0097 T23: -0.0170 REMARK 3 L TENSOR REMARK 3 L11: 3.0523 L22: 7.3396 REMARK 3 L33: 5.9353 L12: -2.8393 REMARK 3 L13: 1.6371 L23: 3.3368 REMARK 3 S TENSOR REMARK 3 S11: 0.0805 S12: 0.3260 S13: -0.0803 REMARK 3 S21: 0.3297 S22: -0.3784 S23: 0.5280 REMARK 3 S31: 0.2641 S32: -1.2973 S33: 0.5190 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 6R6D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292101501. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 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) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS, XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6316 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.838 REMARK 200 RESOLUTION RANGE LOW (A) : 34.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 23.50 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 24.50 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: ORTHORHOMBIC REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1UL 1MM DSDNA, 1UL 5MM REMARK 280 RAC[RU(TAP)2(11,12-CN2-DPPZ)]2+, 6UL OF A SOLUTION CONTAINING 10% REMARK 280 (V/V) 2-METHYL-2,4-PENTANEDIOL, 80MM NACL, 20MM NA-CACODYLATE REMARK 280 PH 7, 20MM BACL2 AND 12MM SPERMINE TETRA-HCL EQUILIBRATED REMARK 280 AGAINST 500UL 35% 2-METHYL-2,4-PENTANEDIOL., VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 17.15400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.35200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.35200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.73100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.35200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.35200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 8.57700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.35200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.35200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.73100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.35200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.35200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 8.57700 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 17.15400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 BA A 101 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 4 O6 REMARK 620 2 HOH A 201 O 68.2 REMARK 620 3 HOH A 202 O 143.4 83.2 REMARK 620 4 HOH A 203 O 130.9 140.7 62.4 REMARK 620 5 HOH A 208 O 66.5 77.9 130.5 138.7 REMARK 620 6 HOH A 210 O 91.3 143.1 124.7 75.9 65.6 REMARK 620 7 HOH A 218 O 129.5 88.5 69.2 95.8 65.0 81.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 103 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 210 O REMARK 620 2 HOH A 210 O 72.6 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BA A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EQQ A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 103 DBREF 6R6D A 1 10 PDB 6R6D 6R6D 1 10 SEQRES 1 A 10 DT DC DG DG DC DG DC DC DG DA HET BA A 101 1 HET EQQ A 102 75 HET NA A 103 1 HETNAM BA BARIUM ION HETNAM EQQ RUTHENIUM (BIS-(TETRAAZAPHENANTHRENE)) (11,12-DICYANO- HETNAM 2 EQQ DIPYRIDOPHENAZINE) HETNAM NA SODIUM ION FORMUL 2 BA BA 2+ FORMUL 3 EQQ C40 H20 N14 RU FORMUL 4 NA NA 1+ FORMUL 5 HOH *18(H2 O) LINK O6 DG A 4 BA BA A 101 1555 1555 2.79 LINK BA BA A 101 O HOH A 201 1555 1555 2.73 LINK BA BA A 101 O HOH A 202 1555 1555 2.73 LINK BA BA A 101 O HOH A 203 1555 1555 2.77 LINK BA BA A 101 O HOH A 208 1555 7555 2.75 LINK BA BA A 101 O HOH A 210 1555 1555 2.70 LINK BA BA A 101 O HOH A 218 1555 1555 2.92 LINK NA NA A 103 O HOH A 210 1555 1555 3.08 LINK NA NA A 103 O HOH A 210 1555 7555 3.17 SITE 1 AC1 8 DG A 3 DG A 4 HOH A 201 HOH A 202 SITE 2 AC1 8 HOH A 203 HOH A 208 HOH A 210 HOH A 218 SITE 1 AC2 9 DT A 1 DC A 2 DG A 3 DG A 4 SITE 2 AC2 9 DC A 5 DC A 7 DC A 8 DG A 9 SITE 3 AC2 9 DA A 10 SITE 1 AC3 3 DG A 4 DC A 5 HOH A 210 CRYST1 46.704 46.704 34.308 90.00 90.00 90.00 P 43 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 0.021411 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021411 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029148 0.00000