HEADER DNA 21-MAY-19 6RSO TITLE STRUCTURE OF [RU(PHEN)2(10-NO2-DPPZ)]2+ BOUND TO THE DNA SEQUENCE TITLE 2 D(TCGGCGCCGA) 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, B; 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 2 10-FEB-21 6RSO 1 TITLE LINK REVDAT 1 08-JUL-20 6RSO 0 JRNL AUTH K.T.MCQUAID,J.P.HALL,C.J.CARDIN JRNL TITL STRUCTURE OF [RU(PHEN)2(10-NO2-DPPZ)]2+ BOUND TO THE DNA JRNL TITL 2 SEQUENCE D(TCGGCGCCGA) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.97 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 9533 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.360 REMARK 3 FREE R VALUE TEST SET COUNT : 511 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 26.3995 - 3.1260 1.00 2261 131 0.1841 0.2271 REMARK 3 2 3.1260 - 2.4818 1.00 2231 116 0.2671 0.3209 REMARK 3 3 2.4818 - 2.1683 1.00 2264 160 0.2145 0.2336 REMARK 3 4 2.1683 - 1.9701 1.00 2266 104 0.3140 0.4023 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.300 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 : 0.008 586 REMARK 3 ANGLE : 0.868 922 REMARK 3 CHIRALITY : 0.039 78 REMARK 3 PLANARITY : 0.008 28 REMARK 3 DIHEDRAL : 23.928 204 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 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.6243 -10.5464 3.1156 REMARK 3 T TENSOR REMARK 3 T11: 0.5187 T22: 0.7386 REMARK 3 T33: 0.6256 T12: 0.0586 REMARK 3 T13: 0.0339 T23: 0.0569 REMARK 3 L TENSOR REMARK 3 L11: 5.9744 L22: 7.3146 REMARK 3 L33: 5.2555 L12: -5.6343 REMARK 3 L13: -7.7371 L23: 5.0267 REMARK 3 S TENSOR REMARK 3 S11: -0.0381 S12: -0.4410 S13: -0.0459 REMARK 3 S21: 0.0787 S22: -0.2073 S23: 0.3346 REMARK 3 S31: -0.0285 S32: -0.5163 S33: 0.2994 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.7985 -11.7460 -4.0657 REMARK 3 T TENSOR REMARK 3 T11: 0.7882 T22: 0.6017 REMARK 3 T33: 0.6567 T12: 0.0357 REMARK 3 T13: -0.0572 T23: -0.0606 REMARK 3 L TENSOR REMARK 3 L11: 5.0786 L22: 5.9021 REMARK 3 L33: 5.1412 L12: -6.3327 REMARK 3 L13: -4.3973 L23: 7.1760 REMARK 3 S TENSOR REMARK 3 S11: -0.1807 S12: 0.1995 S13: -0.2511 REMARK 3 S21: -0.4727 S22: 0.0082 S23: -0.0407 REMARK 3 S31: 0.4396 S32: -0.1039 S33: 0.0569 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 6RSO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1292102519. 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) : 0.9762 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, XDS REMARK 200 DATA SCALING SOFTWARE : XIA2, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9539 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 46.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.9000 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) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 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 : 1.000 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8 UL DROP CONTAINING; 250 UM REMARK 280 D(TCGGCGCCGA), 625 UM RAC-[RU(PHEN)2(10-NO2-DPPZ)]CL2, 7.5% V/V REMARK 280 MPD, 30 MM PH 7 SODIUM CACODYLATE, 9 MM SPERMINE REMARK 280 TETRAHYDROCHLORIDE, 60 MM KCL AND 15 MM BACL2, ALL EQUILIBRATED REMARK 280 AGAINST 500 UL OF 35% V/V MPD, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 15.99500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.99250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 7.99750 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: 2180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 BA A 101 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 4 O6 REMARK 620 2 HOH A 201 O 147.8 REMARK 620 3 HOH A 202 O 91.7 116.5 REMARK 620 4 HOH A 204 O 132.8 61.0 60.0 REMARK 620 5 HOH A 207 O 71.1 88.1 150.1 148.6 REMARK 620 6 HOH A 212 O 130.7 70.3 85.3 86.9 87.8 REMARK 620 7 HOH B 205 O 62.8 132.9 81.2 135.7 69.2 68.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA B 101 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 205 O REMARK 620 2 DG B 4 O6 60.8 REMARK 620 3 HOH B 201 O 132.5 145.9 REMARK 620 4 HOH B 203 O 82.1 96.9 114.9 REMARK 620 5 HOH B 204 O 139.0 129.1 65.9 58.3 REMARK 620 6 HOH B 208 O 68.4 69.5 86.3 150.5 150.1 REMARK 620 7 HOH B 218 O 71.0 131.4 68.8 81.1 91.1 88.8 REMARK 620 N 1 2 3 4 5 6 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 KHN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BA B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KHN B 102 DBREF 6RSO A 1 10 PDB 6RSO 6RSO 1 10 DBREF 6RSO B 1 10 PDB 6RSO 6RSO 1 10 SEQRES 1 A 10 DT DC DG DG DC DG DC DC DG DA SEQRES 1 B 10 DT DC DG DG DC DG DC DC DG DA HET BA A 101 1 HET KHN A 102 79 HET BA B 101 1 HET KHN B 102 79 HETNAM BA BARIUM ION HETNAM KHN RUTHENIUM (BIS-(PHENANTHROLINE)) (10-NITRO- HETNAM 2 KHN DIPYRIDOPHENAZINE) FORMUL 3 BA 2(BA 2+) FORMUL 4 KHN 2(C42 H26 N9 O2 RU) FORMUL 7 HOH *30(H2 O) LINK O6 DG A 4 BA BA A 101 1555 1555 2.86 LINK BA BA A 101 O HOH A 201 1555 1555 2.62 LINK BA BA A 101 O HOH A 202 1555 1555 2.76 LINK BA BA A 101 O HOH A 204 1555 1555 2.68 LINK BA BA A 101 O HOH A 207 1555 1555 2.57 LINK BA BA A 101 O HOH A 212 1555 1555 2.95 LINK BA BA A 101 O HOH B 205 1555 1555 2.93 LINK O HOH A 205 BA BA B 101 1555 1555 2.84 LINK O6 DG B 4 BA BA B 101 1555 1555 2.89 LINK BA BA B 101 O HOH B 201 1555 1555 2.58 LINK BA BA B 101 O HOH B 203 1555 1555 2.83 LINK BA BA B 101 O HOH B 204 1555 1555 2.73 LINK BA BA B 101 O HOH B 208 1555 1555 2.57 LINK BA BA B 101 O HOH B 218 1555 1555 2.75 SITE 1 AC1 8 DG A 3 DG A 4 HOH A 201 HOH A 202 SITE 2 AC1 8 HOH A 204 HOH A 207 HOH A 212 HOH B 205 SITE 1 AC2 8 DC A 7 DC A 8 DG A 9 DA A 10 SITE 2 AC2 8 DT B 1 DC B 2 DG B 3 DG B 4 SITE 1 AC3 8 HOH A 205 DG B 3 DG B 4 HOH B 201 SITE 2 AC3 8 HOH B 203 HOH B 204 HOH B 208 HOH B 218 SITE 1 AC4 9 DT A 1 DC A 2 DG A 3 DG A 4 SITE 2 AC4 9 DC A 5 DC B 7 DC B 8 DG B 9 SITE 3 AC4 9 DA B 10 CRYST1 46.730 46.730 31.990 90.00 90.00 90.00 P 43 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 0.021400 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021400 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031260 0.00000