HEADER DNA 08-JUN-20 6XCL TITLE CRYSTAL STRUCTURE OF HUMAN TELOMERIC DNA G-QUADRUPLEX IN COMPLEX WITH TITLE 2 A NOVEL PLATINUM(II) COMPLEX. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)- COMPND 4 3'); COMPND 5 CHAIN: A, B; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS GUANINE QUADRUPLEX, LIGAND COMPLEX, DNA EXPDTA X-RAY DIFFRACTION AUTHOR C.E.MIRON,L.M.VAN STAALDUINEN,Z.JIA,A.PETITJEAN REVDAT 3 18-OCT-23 6XCL 1 REMARK REVDAT 2 03-FEB-21 6XCL 1 JRNL REVDAT 1 04-NOV-20 6XCL 0 JRNL AUTH C.E.MIRON,L.VAN STAALDUINEN,A.M.RANGASWAMY,M.CHEN,Y.LIANG, JRNL AUTH 2 Z.JIA,J.L.MERGNY,A.PETITJEAN JRNL TITL GOING PLATINUM TO THE TUNE OF A REMARKABLE GUANINE JRNL TITL 2 QUADRUPLEX BINDER: SOLUTION- AND SOLID-STATE INVESTIGATIONS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 60 2500 2021 JRNL REFN ESSN 1521-3773 JRNL PMID 33090592 JRNL DOI 10.1002/ANIE.202012520 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.1_3865 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 10574 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 530 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 33.6000 - 4.2900 0.99 2513 134 0.1476 0.2117 REMARK 3 2 4.2800 - 3.4000 1.00 2520 132 0.2104 0.2245 REMARK 3 3 3.4000 - 2.9700 0.98 2489 132 0.2051 0.2989 REMARK 3 4 2.9700 - 2.7000 1.00 2522 132 0.3133 0.3343 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) : 0.327 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.956 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.07 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 : 0.010 1156 REMARK 3 ANGLE : 1.158 1766 REMARK 3 CHIRALITY : 0.045 174 REMARK 3 PLANARITY : 0.006 56 REMARK 3 DIHEDRAL : 34.561 440 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 6XCL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000249897. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10637 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09700 REMARK 200 FOR THE DATA SET : 14.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.81600 REMARK 200 FOR SHELL : 2.510 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: 3T5E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM KCL, 10 MM MGCL2, 50 MM MES (PH REMARK 280 6.0), 10% PEG 400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z 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 0.00000 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 0.00000 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 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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG A 21 O4' - C1' - N9 ANGL. DEV. = 1.9 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 A 104 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 2 O6 REMARK 620 2 DG A 3 O6 79.0 REMARK 620 3 DG A 8 O6 68.7 88.0 REMARK 620 4 DG A 9 O6 127.6 63.7 74.2 REMARK 620 5 DG A 14 O6 121.1 148.3 78.8 84.9 REMARK 620 6 DG A 15 O6 161.9 97.3 129.1 63.7 70.6 REMARK 620 7 DG A 20 O6 82.2 137.1 120.1 149.8 73.4 89.0 REMARK 620 8 DG A 21 O6 92.4 58.7 144.9 97.6 135.4 71.0 84.2 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 105 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 3 O6 REMARK 620 2 DG A 4 O6 69.3 REMARK 620 3 DG A 9 O6 65.4 90.9 REMARK 620 4 DG A 10 O6 128.1 82.1 73.0 REMARK 620 5 DG A 15 O6 104.0 155.7 65.7 84.7 REMARK 620 6 DG A 16 O6 154.3 123.7 130.2 77.4 72.5 REMARK 620 7 DG A 21 O6 60.4 118.4 98.1 158.2 73.6 94.9 REMARK 620 8 DG A 22 O6 92.0 79.0 157.3 124.7 125.1 71.4 70.0 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 106 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 6 O2 REMARK 620 2 DT A 18 O2 64.5 REMARK 620 3 EDO A 102 O1 68.8 4.5 REMARK 620 4 EDO A 102 O2 64.8 4.2 4.8 REMARK 620 5 DT B 6 O2 132.7 68.3 63.9 67.9 REMARK 620 6 DT B 18 O2 68.3 7.5 5.1 4.1 64.5 REMARK 620 7 EDO B 501 O1 66.1 5.2 4.5 1.4 66.6 2.6 REMARK 620 8 EDO B 501 O2 67.2 2.8 1.7 4.3 65.5 5.9 4.4 REMARK 620 9 HOH B 601 O 68.4 3.9 1.8 5.8 64.4 6.9 5.8 1.6 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 504 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 2 O6 REMARK 620 2 DG B 3 O6 77.8 REMARK 620 3 DG B 8 O6 69.8 90.4 REMARK 620 4 DG B 9 O6 132.6 71.6 75.1 REMARK 620 5 DG B 14 O6 115.6 153.4 74.5 83.2 REMARK 620 6 DG B 15 O6 154.7 102.6 135.2 69.2 75.2 REMARK 620 7 DG B 20 O6 73.2 131.7 113.8 152.5 74.9 89.0 REMARK 620 8 DG B 21 O6 88.7 61.1 147.9 106.3 137.5 70.3 80.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 502 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 3 O6 REMARK 620 2 DG B 4 O6 67.9 REMARK 620 3 DG B 9 O6 65.7 90.2 REMARK 620 4 DG B 10 O6 127.5 81.9 72.8 REMARK 620 5 DG B 15 O6 98.6 153.3 63.0 89.6 REMARK 620 6 DG B 16 O6 150.6 130.5 127.5 81.1 72.2 REMARK 620 7 DG B 21 O6 58.7 118.3 94.0 156.5 66.9 92.5 REMARK 620 8 DG B 22 O6 86.8 80.9 152.4 130.7 122.6 76.0 68.2 REMARK 620 N 1 2 3 4 5 6 7 DBREF 6XCL A 1 22 PDB 6XCL 6XCL 1 22 DBREF 6XCL B 1 22 PDB 6XCL 6XCL 1 22 SEQRES 1 A 22 DA DG DG DG DT DT DA DG DG DG DT DT DA SEQRES 2 A 22 DG DG DG DT DT DA DG DG DG SEQRES 1 B 22 DA DG DG DG DT DT DA DG DG DG DT DT DA SEQRES 2 B 22 DG DG DG DT DT DA DG DG DG HET V4A A 101 31 HET EDO A 102 4 HET V4A A 103 31 HET K A 104 1 HET K A 105 1 HET K A 106 1 HET EDO B 501 4 HET K B 502 1 HET V4A B 503 31 HET K B 504 1 HETNAM V4A PLATINUM(II) BIS[3-(PYRIDIN-2-YL)-[1,2,4]TRIAZOLO[4,3- HETNAM 2 V4A A]PYRIDINE] HETNAM EDO 1,2-ETHANEDIOL HETNAM K POTASSIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 V4A 3(C22 H16 N8 PT 2+) FORMUL 4 EDO 2(C2 H6 O2) FORMUL 6 K 5(K 1+) FORMUL 13 HOH *6(H2 O) LINK O6 DG A 2 K K A 104 1555 1555 2.59 LINK O6 DG A 3 K K A 104 1555 1555 2.96 LINK O6 DG A 3 K K A 105 1555 1555 2.83 LINK O6 DG A 4 K K A 105 1555 1555 2.75 LINK O2 DT A 6 K K A 106 1555 1554 3.10 LINK O6 DG A 8 K K A 104 1555 1555 2.79 LINK O6 DG A 9 K K A 104 1555 1555 3.04 LINK O6 DG A 9 K K A 105 1555 1555 3.03 LINK O6 DG A 10 K K A 105 1555 1555 2.56 LINK O6 DG A 14 K K A 104 1555 1555 2.71 LINK O6 DG A 15 K K A 104 1555 1555 3.14 LINK O6 DG A 15 K K A 105 1555 1555 2.98 LINK O6 DG A 16 K K A 105 1555 1555 2.87 LINK O2 DT A 18 K K A 106 1555 1555 3.01 LINK O6 DG A 20 K K A 104 1555 1555 2.56 LINK O6 DG A 21 K K A 104 1555 1555 2.78 LINK O6 DG A 21 K K A 105 1555 1555 2.77 LINK O6 DG A 22 K K A 105 1555 1555 2.77 LINK O1 EDO A 102 K K A 106 1555 1555 3.32 LINK O2 EDO A 102 K K A 106 1555 1555 2.98 LINK K K A 106 O2 DT B 6 1554 1555 2.96 LINK K K A 106 O2 DT B 18 1555 1555 2.96 LINK K K A 106 O1 EDO B 501 1555 1556 3.15 LINK K K A 106 O2 EDO B 501 1555 1556 3.32 LINK K K A 106 O HOH B 601 1555 1556 3.02 LINK K K A 106 O HOH B 602 1555 1556 2.91 LINK O6 DG B 2 K K B 504 1555 1555 2.75 LINK O6 DG B 3 K K B 502 1555 1555 3.00 LINK O6 DG B 3 K K B 504 1555 1555 2.93 LINK O6 DG B 4 K K B 502 1555 1555 2.67 LINK O6 DG B 8 K K B 504 1555 1555 2.94 LINK O6 DG B 9 K K B 502 1555 1555 3.26 LINK O6 DG B 9 K K B 504 1555 1555 2.88 LINK O6 DG B 10 K K B 502 1555 1555 2.57 LINK O6 DG B 14 K K B 504 1555 1555 2.90 LINK O6 DG B 15 K K B 502 1555 1555 3.02 LINK O6 DG B 15 K K B 504 1555 1555 2.92 LINK O6 DG B 16 K K B 502 1555 1555 2.66 LINK O6 DG B 20 K K B 504 1555 1555 2.67 LINK O6 DG B 21 K K B 502 1555 1555 2.92 LINK O6 DG B 21 K K B 504 1555 1555 2.77 LINK O6 DG B 22 K K B 502 1555 1555 2.73 CRYST1 64.030 64.030 42.230 90.00 90.00 120.00 P 3 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 0.015618 0.009017 0.000000 0.00000 SCALE2 0.000000 0.018034 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023680 0.00000