PDB Short entry for 4JD8 HEADER DNA 24-FEB-13 4JD8 TITLE RACEMIC-[RU(PHEN)2(DPPZ)]2+] BOUND TO SYNTHETIC DNA AT HIGH RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*TP*GP*CP*AP*T)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: DNA PURCHASED FROM ATDBIO KEYWDS INTERCALATION, RACEMIC LIGAND-DNA, DNA EXPDTA X-RAY DIFFRACTION AUTHOR D.S.COOK,J.P.HALL,C.J.CARDIN REVDAT 3 20-SEP-23 4JD8 1 REMARK LINK REVDAT 2 18-SEP-13 4JD8 1 JRNL REVDAT 1 24-APR-13 4JD8 0 SPRSDE 24-APR-13 4JD8 4E87 JRNL AUTH J.P.HALL,D.COOK,S.R.MORTE,P.MCINTYRE,K.BUCHNER,H.BEER, JRNL AUTH 2 D.J.CARDIN,J.A.BRAZIER,G.WINTER,J.M.KELLY,C.J.CARDIN JRNL TITL X-RAY CRYSTAL STRUCTURE OF RAC-[RU(PHEN)2DPPZ](2+) WITH JRNL TITL 2 D(ATGCAT)2 SHOWS ENANTIOMER ORIENTATIONS AND WATER ORDERING. JRNL REF J.AM.CHEM.SOC. V. 135 12652 2013 JRNL REFN ISSN 0002-7863 JRNL PMID 23875832 JRNL DOI 10.1021/JA403590E REMARK 2 REMARK 2 RESOLUTION. 1.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 15678 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.139 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 789 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 32.5319 - 2.1023 0.97 2605 123 0.1404 0.1607 REMARK 3 2 2.1023 - 1.6687 0.99 2505 137 0.1230 0.1346 REMARK 3 3 1.6687 - 1.4577 0.99 2488 128 0.1050 0.1515 REMARK 3 4 1.4577 - 1.3244 0.98 2440 134 0.1332 0.1811 REMARK 3 5 1.3244 - 1.2295 0.98 2431 125 0.1852 0.2273 REMARK 3 6 1.2295 - 1.1570 0.98 2420 142 0.2298 0.2602 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.350 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 : 0.015 396 REMARK 3 ANGLE : 2.966 628 REMARK 3 CHIRALITY : 0.091 46 REMARK 3 PLANARITY : 0.029 18 REMARK 3 DIHEDRAL : 32.509 122 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 4JD8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000077899. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 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) : 0.9795 REMARK 200 MONOCHROMATOR : DUAL SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15712 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.160 REMARK 200 RESOLUTION RANGE LOW (A) : 32.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 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: PHASER REMARK 200 STARTING MODEL: 4E87 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1UL, 1MM D(ATGCAT)2 1UL, 3MM RAC REMARK 280 -[RU(PHEN)2DPPZ]2CL 6UL, 40MM SPERMINE, 40MM SODIUM CACODYLATE REMARK 280 PH 6.3, 10% MPD (V/V), 80 MM KCL, 20 MM BACL2, 1ML OF 35% MPD, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 18.12367 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 36.24733 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 36.24733 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 18.12367 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, 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 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 B 103 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 248 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 B 240 O HOH B 243 1.61 REMARK 500 O HOH A 110 O HOH A 141 1.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 137 O HOH B 243 3454 2.08 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 2 O5' - P - OP2 ANGL. DEV. = -7.4 DEGREES REMARK 500 DT A 6 O5' - P - OP1 ANGL. DEV. = 11.0 DEGREES REMARK 500 DT A 6 O5' - P - OP2 ANGL. DEV. = -8.3 DEGREES REMARK 500 DT A 6 C1' - O4' - C4' ANGL. DEV. = -8.0 DEGREES REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC B 4 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 B 103 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC B 4 OP1 REMARK 620 2 HOH B 216 O 83.5 REMARK 620 3 HOH B 241 O 70.8 63.5 REMARK 620 4 HOH B 245 O 80.0 72.7 129.1 REMARK 620 5 HOH B 248 O 142.7 70.5 116.8 67.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0TN B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RKP B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DX4 RELATED DB: PDB REMARK 900 LOWER RESOLUTION MODEL REMARK 900 RELATED ID: 4E7Y RELATED DB: PDB REMARK 900 RELATED ID: 4E87 RELATED DB: PDB REMARK 900 RELATED ID: 4E8S RELATED DB: PDB REMARK 900 RELATED ID: 4E8X RELATED DB: PDB REMARK 900 RELATED ID: 4E95 RELATED DB: PDB DBREF 4JD8 A 1 6 PDB 4JD8 4JD8 1 6 DBREF 4JD8 B 1 6 PDB 4JD8 4JD8 1 6 SEQRES 1 A 6 DA DT DG DC DA DT SEQRES 1 B 6 DA DT DG DC DA DT HET 0TN B 101 77 HET RKP B 102 77 HET K B 103 1 HETNAM 0TN DELTA-RU(PHEN)2(DPPZ) COMPLEX HETNAM RKP LAMBDA-RU(PHEN)2(DPPZ) COMPLEX HETNAM K POTASSIUM ION FORMUL 3 0TN C42 H26 N8 RU FORMUL 4 RKP C42 H26 N8 RU FORMUL 5 K K 1+ FORMUL 6 HOH *95(H2 O) LINK OP1 DC B 4 K K B 103 1555 1555 2.71 LINK K K B 103 O HOH B 216 1555 1555 2.88 LINK K K B 103 O HOH B 241 1555 1555 2.99 LINK K K B 103 O HOH B 245 1555 1555 2.61 LINK K K B 103 O HOH B 248 1555 1555 2.79 SITE 1 AC1 8 DT A 2 DG A 3 DC A 4 DT A 6 SITE 2 AC1 8 DA B 1 DC B 4 DA B 5 DT B 6 SITE 1 AC2 8 DA A 1 DC A 4 DA A 5 DT A 6 SITE 2 AC2 8 DT B 2 DG B 3 DA B 5 DT B 6 SITE 1 AC3 5 DC B 4 HOH B 216 HOH B 241 HOH B 245 SITE 2 AC3 5 HOH B 248 CRYST1 37.550 37.550 54.371 90.00 90.00 120.00 P 31 2 1 12 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 0.026631 0.015376 0.000000 0.00000 SCALE2 0.000000 0.030751 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018392 0.00000