HEADER DNA 25-JUL-18 6H5R TITLE STRUCTURE OF THE COMPLEX OF A HUMAN TELOMERIC DNA WITH BIS(1-BUTYL-3- TITLE 2 METHYL-IMIDAZOLE-2-YLIDENE) GOLD(I) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN TELOMERIC DNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS DRUG-DNA COMPLEX, G QUADRUPLEX, DNA EXPDTA X-RAY DIFFRACTION AUTHOR C.BAZZICALUPI,P.GRATTERI,F.PAPI REVDAT 2 17-JAN-24 6H5R 1 REMARK LINK REVDAT 1 30-JAN-19 6H5R 0 JRNL AUTH F.GUARRA,T.MARZO,M.FERRARONI,F.PAPI,C.BAZZICALUPI, JRNL AUTH 2 P.GRATTERI,G.PESCITELLI,L.MESSORI,T.BIVER,C.GABBIANI JRNL TITL INTERACTION OF A GOLD(I) DICARBENE ANTICANCER DRUG WITH JRNL TITL 2 HUMAN TELOMERIC DNA G-QUADRUPLEX: SOLUTION AND JRNL TITL 3 COMPUTATIONALLY AIDED X-RAY DIFFRACTION ANALYSIS. JRNL REF DALTON TRANS V. 47 16132 2018 JRNL REFN ESSN 1477-9234 JRNL PMID 30378627 JRNL DOI 10.1039/C8DT03607A REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 4178 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 11.000 REMARK 3 FREE R VALUE TEST SET COUNT : 517 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 504 REMARK 3 HETEROGEN ATOMS : 87 REMARK 3 SOLVENT ATOMS : 39 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.51000 REMARK 3 B22 (A**2) : 4.10000 REMARK 3 B33 (A**2) : -3.58000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.12000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.290 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.204 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.140 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.018 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6H5R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1200011084. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.872900 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8883 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 35.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11000 REMARK 200 FOR THE DATA SET : 6.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 2.65000 REMARK 200 R SYM FOR SHELL (I) : 0.60000 REMARK 200 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: MOLREP REMARK 200 STARTING MODEL: 3R6R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ISOPROPANOL, KCACODYLATE, LI2SO4, REMARK 280 MGSO4, PH 6.5, VAPOR DIFFUSION, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 18.30000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.68500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 18.30000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.68500 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -131.0 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 -1.000000 0.000000 0.000000 -1.14217 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 27.02588 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 216 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DT A 24 O3' REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 FTQ A 105 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 102 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 3 O6 REMARK 620 2 DG A 4 O6 77.9 REMARK 620 3 DG A 9 O6 70.7 88.9 REMARK 620 4 DG A 10 O6 133.0 68.8 76.4 REMARK 620 5 DG A 15 O6 109.4 154.1 71.2 90.0 REMARK 620 6 DG A 16 O6 153.4 107.0 134.4 70.7 77.9 REMARK 620 7 DG A 21 O6 71.1 134.6 110.2 154.1 69.8 88.7 REMARK 620 8 DG A 22 O6 89.6 70.4 154.3 108.4 132.8 68.6 76.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR A 103 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 3 O6 REMARK 620 2 DG A 9 O6 76.2 REMARK 620 3 DG A 15 O6 121.3 76.7 REMARK 620 4 DG A 21 O6 76.9 122.3 75.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 4 O6 REMARK 620 2 DG A 5 O6 71.3 REMARK 620 3 DG A 10 O6 68.8 88.3 REMARK 620 4 DG A 11 O6 126.7 75.5 69.8 REMARK 620 5 DG A 16 O6 105.5 158.0 70.7 90.7 REMARK 620 6 DG A 17 O6 157.9 120.6 126.5 75.3 70.5 REMARK 620 7 DG A 22 O6 69.4 127.6 107.9 156.9 67.6 89.5 REMARK 620 8 DG A 23 O6 89.2 74.0 155.5 119.9 128.0 77.7 72.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SR A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FTQ A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FTQ A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FTQ A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FTQ A 107 DBREF 6H5R A 1 24 PDB 6H5R 6H5R 1 24 SEQRES 1 A 24 DT DA DG DG DG DT DT DA DG DG DG DT DT SEQRES 2 A 24 DA DG DG DG DT DT DA DG DG DG DT HET K A 101 1 HET K A 102 1 HET SR A 103 1 HET FTQ A 104 21 HET FTQ A 105 21 HET FTQ A 106 21 HET FTQ A 107 21 HETNAM K POTASSIUM ION HETNAM SR STRONTIUM ION HETNAM FTQ BIS(1-BUTYL-3-METHYL-IMIDAZOL-3-IUM-2-YL)GOLD FORMUL 2 K 2(K 1+) FORMUL 4 SR SR 2+ FORMUL 5 FTQ 4(C16 H28 AU N4 2+) FORMUL 9 HOH *39(H2 O) LINK O6 DG A 3 K K A 102 1555 1555 2.74 LINK O6 DG A 3 SR SR A 103 1555 2556 2.57 LINK O6 DG A 4 K K A 101 1555 1555 2.92 LINK O6 DG A 4 K K A 102 1555 1555 2.90 LINK O6 DG A 5 K K A 101 1555 1555 2.75 LINK O6 DG A 9 K K A 102 1555 1555 2.77 LINK O6 DG A 9 SR SR A 103 1555 2556 2.60 LINK O6 DG A 10 K K A 101 1555 1555 2.98 LINK O6 DG A 10 K K A 102 1555 1555 3.01 LINK O6 DG A 11 K K A 101 1555 1555 2.68 LINK O6 DG A 15 K K A 102 1555 1555 2.75 LINK O6 DG A 15 SR SR A 103 1555 2556 2.58 LINK O6 DG A 16 K K A 101 1555 1555 2.91 LINK O6 DG A 16 K K A 102 1555 1555 2.88 LINK O6 DG A 17 K K A 101 1555 1555 2.69 LINK O6 DG A 21 K K A 102 1555 1555 2.79 LINK O6 DG A 21 SR SR A 103 1555 2556 2.60 LINK O6 DG A 22 K K A 101 1555 1555 2.96 LINK O6 DG A 22 K K A 102 1555 1555 2.92 LINK O6 DG A 23 K K A 101 1555 1555 2.66 SITE 1 AC1 9 DG A 4 DG A 5 DG A 10 DG A 11 SITE 2 AC1 9 DG A 16 DG A 17 DG A 22 DG A 23 SITE 3 AC1 9 K A 102 SITE 1 AC2 10 DG A 3 DG A 4 DG A 9 DG A 10 SITE 2 AC2 10 DG A 15 DG A 16 DG A 21 DG A 22 SITE 3 AC2 10 K A 101 SR A 103 SITE 1 AC3 5 DG A 3 DG A 9 DG A 15 DG A 21 SITE 2 AC3 5 K A 102 SITE 1 AC4 9 DG A 5 DG A 11 DG A 17 DT A 18 SITE 2 AC4 9 DG A 23 DT A 24 FTQ A 105 FTQ A 106 SITE 3 AC4 9 FTQ A 107 SITE 1 AC5 7 DG A 5 DG A 11 DG A 17 DT A 24 SITE 2 AC5 7 FTQ A 104 FTQ A 106 FTQ A 107 SITE 1 AC6 9 DG A 5 DT A 6 DG A 11 DT A 12 SITE 2 AC6 9 DG A 17 DG A 23 FTQ A 104 FTQ A 105 SITE 3 AC6 9 FTQ A 107 SITE 1 AC7 10 DG A 5 DG A 11 DT A 12 DG A 17 SITE 2 AC7 10 DT A 18 DG A 23 DT A 24 FTQ A 104 SITE 3 AC7 10 FTQ A 105 FTQ A 106 CRYST1 36.600 71.370 27.050 90.00 92.42 90.00 C 1 2 1 4 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 0.027322 0.000000 0.001155 0.00000 SCALE2 0.000000 0.014011 0.000000 0.00000 SCALE3 0.000000 0.000000 0.037002 0.00000