PDB Short entry for 5JEU HEADER DNA 19-APR-16 5JEU TITLE DEL-[RU(PHEN)2(DPPZ)]2+ BOUND TO D(TCGGCGCCGA) WITH BA2+ 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 DNA, RUTHENIUM, LIGHT-SWITCH, SEMI-INTERCALATION EXPDTA X-RAY DIFFRACTION AUTHOR J.P.HALL,C.J.CARDIN REVDAT 4 09-NOV-16 5JEU 1 JRNL REVDAT 3 28-SEP-16 5JEU 1 JRNL REVDAT 2 21-SEP-16 5JEU 1 JRNL REVDAT 1 14-SEP-16 5JEU 0 JRNL AUTH J.P.HALL,P.M.KEANE,H.BEER,K.BUCHNER,G.WINTER,T.L.SORENSEN, JRNL AUTH 2 D.J.CARDIN,J.A.BRAZIER,C.J.CARDIN JRNL TITL DELTA CHIRALITY RUTHENIUM 'LIGHT-SWITCH' COMPLEXES CAN BIND JRNL TITL 2 IN THE MINOR GROOVE OF DNA WITH FIVE DIFFERENT BINDING JRNL TITL 3 MODES. JRNL REF NUCLEIC ACIDS RES. V. 44 9472 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 27599841 JRNL DOI 10.1093/NAR/GKW753 REMARK 2 REMARK 2 RESOLUTION. 0.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 38325 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.113 REMARK 3 R VALUE (WORKING SET) : 0.113 REMARK 3 FREE R VALUE : 0.127 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1905 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 25.1854 - 2.3374 0.94 2550 130 0.1146 0.1371 REMARK 3 2 2.3374 - 1.8555 0.94 2571 129 0.1071 0.1128 REMARK 3 3 1.8555 - 1.6210 0.94 2528 142 0.0916 0.1145 REMARK 3 4 1.6210 - 1.4728 0.94 2566 124 0.0816 0.0875 REMARK 3 5 1.4728 - 1.3672 0.94 2581 140 0.0877 0.0851 REMARK 3 6 1.3672 - 1.2866 0.95 2538 131 0.0872 0.0972 REMARK 3 7 1.2866 - 1.2222 0.96 2635 126 0.0968 0.1069 REMARK 3 8 1.2222 - 1.1690 0.97 2587 151 0.1134 0.1219 REMARK 3 9 1.1690 - 1.1240 0.97 2655 125 0.1269 0.1245 REMARK 3 10 1.1240 - 1.0852 0.98 2592 158 0.1524 0.1741 REMARK 3 11 1.0852 - 1.0513 0.98 2649 124 0.1815 0.1824 REMARK 3 12 1.0513 - 1.0212 0.98 2680 133 0.2054 0.2342 REMARK 3 13 1.0212 - 0.9943 0.98 2628 147 0.2405 0.2732 REMARK 3 14 0.9943 - 0.9701 0.97 2660 145 0.2652 0.2769 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.450 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 : 0.013 373 REMARK 3 ANGLE : 2.525 595 REMARK 3 CHIRALITY : 0.067 42 REMARK 3 PLANARITY : 0.028 17 REMARK 3 DIHEDRAL : 28.643 115 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5JEU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220439. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-12 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 : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8266 REMARK 200 MONOCHROMATOR : DUAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS, XIA2 REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20581 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.970 REMARK 200 RESOLUTION RANGE LOW (A) : 25.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.02700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.85700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1UL 4MM DEL-[RU(PHEN)2(DPPZ)]2+, 1UL REMARK 280 2MM D(TCGGCGCCGA), 6UL OF A SOLUTION CONTAINING 40MM NA- REMARK 280 CACODYLATE PH 7, 12MM SPERMINE, 80MM KCL, 20MM BACL2, 10% (V/V) REMARK 280 HEXYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 14.71500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.31000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.31000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 7.35750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.31000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.31000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.07250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.31000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.31000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 7.35750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.31000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.31000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.07250 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 14.71500 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 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 APPLY THE FOLLOWING TO CHAINS: A 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 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 HOH A 232 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 244 O HOH A 268 2.17 REMARK 500 O2 DT A 1 O HOH A 201 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 273 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A 274 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A 275 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A 276 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A 277 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH A 278 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH A 279 DISTANCE = 7.52 ANGSTROMS REMARK 525 HOH A 280 DISTANCE = 7.54 ANGSTROMS REMARK 525 HOH A 281 DISTANCE = 9.37 ANGSTROMS REMARK 525 HOH A 282 DISTANCE = 11.79 ANGSTROMS 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 233 O 64.5 REMARK 620 3 HOH A 252 O 131.0 66.9 REMARK 620 4 HOH A 210 O 72.4 82.1 95.5 REMARK 620 5 HOH A 223 O 125.9 137.5 94.5 139.4 REMARK 620 6 HOH A 248 O 113.7 71.1 53.1 144.6 67.5 REMARK 620 7 HOH A 222 O 147.6 129.1 67.8 80.4 67.4 98.6 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 0TN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 0TN A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 104 DBREF 5JEU A 1 10 PDB 5JEU 5JEU 1 10 SEQRES 1 A 10 DT DC DG DG DC DG DC DC DG DA HET BA A 101 1 HET 0TN A 102 77 HET 0TN A 103 77 HET CL A 104 1 HETNAM BA BARIUM ION HETNAM 0TN DELTA-RU(PHEN)2(DPPZ) COMPLEX HETNAM CL CHLORIDE ION FORMUL 2 BA BA 2+ FORMUL 3 0TN 2(C42 H26 N8 RU) FORMUL 5 CL CL 1- FORMUL 6 HOH *82(H2 O) LINK O6 DG A 4 BA BA A 101 1555 1555 2.92 LINK BA BA A 101 O HOH A 233 1555 1555 2.78 LINK BA BA A 101 O HOH A 252 1555 1555 2.67 LINK BA BA A 101 O HOH A 210 1555 1555 2.77 LINK BA BA A 101 O HOH A 223 1555 1555 2.88 LINK BA BA A 101 O HOH A 248 1555 1555 2.74 LINK BA BA A 101 O HOH A 222 1555 1555 2.79 SITE 1 AC1 8 DG A 3 DG A 4 HOH A 210 HOH A 222 SITE 2 AC1 8 HOH A 223 HOH A 233 HOH A 248 HOH A 252 SITE 1 AC2 5 DT A 1 DC A 2 DG A 3 DG A 9 SITE 2 AC2 5 DA A 10 SITE 1 AC3 7 DG A 3 DG A 4 DC A 7 DC A 8 SITE 2 AC3 7 DG A 9 DA A 10 HOH A 235 SITE 1 AC4 3 DG A 3 DA A 10 HOH A 255 CRYST1 48.620 48.620 29.430 90.00 90.00 90.00 P 41 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 0.020568 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020568 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033979 0.00000