HEADER DNA 30-OCT-20 7ATG TITLE CRYSTAL STRUCTURE OF Z-DNA IN COMPLEX WITH PUTRESCINIUM AND POTASSIUM TITLE 2 CATIONS AT ULTRAHIGH-RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*CP*G)-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 Z-DNA, DNA, DUAL-CONFORMATION BACKBONE; PUTRESCINIUM CATION; BIOGENIC KEYWDS 2 POLYAMINES; POTASSIUM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.DROZDZAL,M.GILSKI,M.JASKOLSKI REVDAT 3 31-JAN-24 7ATG 1 REMARK REVDAT 2 06-OCT-21 7ATG 1 JRNL REVDAT 1 11-AUG-21 7ATG 0 JRNL AUTH P.DROZDZAL,M.GILSKI,M.JASKOLSKI JRNL TITL CRYSTAL STRUCTURE OF Z-DNA IN COMPLEX WITH THE POLYAMINE JRNL TITL 2 PUTRESCINE AND POTASSIUM CATIONS AT ULTRA-HIGH RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.B V. 77 331 2021 JRNL REFN ESSN 2052-5206 JRNL PMID 34096514 JRNL DOI 10.1107/S2052520621002663 REMARK 2 REMARK 2 RESOLUTION. 0.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 240 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 123 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 333.73 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 141.29 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 3 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 3962 REMARK 3 NUMBER OF RESTRAINTS : 4374 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 1.560 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.005 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.089 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.061 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.070 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE REFINEMENT WAS CARRIED OUT AGAINST REMARK 3 SEPARATE BIJVOET PAIRS. HYDROGEN ATOMS WERE ADDED AT RIDING REMARK 3 POSITIONS. THE FINAL REFINEMENT WAS CALCULATED USING WEIGHTED FULL- REMARK 3 MATRIX LEAST-SQUARES PROCEDURE. CONFORMATION-DEPENDENT GEOMETRICAL REMARK 3 RESTRAINTS ON BOND LENGTHS AND BOND ANGLES FOR POLYNUCLEOTIDE REMARK 3 CHAINS WERE GENERATED USING THE RESTRAINTLIB SERVER: HTTP:// REMARK 3 ACHESYM.IBCH.POZNAN.PL/RESTRAINTLIB/ REMARK 4 REMARK 4 7ATG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1292109990. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-15; 22-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY; PETRA REMARK 200 III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1); P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.72930; 0.7293 REMARK 200 MONOCHROMATOR : SI(111); SI(111) REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M; DECTRIS REMARK 200 PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 107989 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.600 REMARK 200 RESOLUTION RANGE LOW (A) : 25.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.02400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.8400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 22.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.20 REMARK 200 R MERGE FOR SHELL (I) : 0.26400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.880 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4HIG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10%(V/V) (+/-)-2-METHYL-2,4 REMARK 280 -PENTANEDIOL (MPD), 40 MM SODIUM CACODYLATE PH 6.0, 80 MM KCL, REMARK 280 12 MM NACL, 14 MM PUTRESCINIUM DICHLORIDE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 8.98500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.93000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.51000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.93000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 8.98500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.51000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 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 259 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH B 264 DISTANCE = 5.85 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 K A 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 6 OP1 REMARK 620 2 DG A 6 O5' 49.5 REMARK 620 3 HOH A 217 O 108.8 73.4 REMARK 620 4 HOH A 248 O 97.1 123.6 80.3 REMARK 620 5 DC B 9 OP1 15.1 34.5 98.4 106.5 REMARK 620 6 DC B 9 OP2 19.6 30.2 93.1 106.6 5.3 REMARK 620 7 HOH B 255 O 49.7 79.6 153.0 114.9 56.9 61.8 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HIG RELATED DB: PDB REMARK 900 RELATED ID: 4HIF RELATED DB: PDB REMARK 900 RELATED ID: 4R15 RELATED DB: PDB DBREF 7ATG A 1 6 PDB 7ATG 7ATG 1 6 DBREF 7ATG B 7 12 PDB 7ATG 7ATG 7 12 SEQRES 1 A 6 DC DG DC DG DC DG SEQRES 1 B 6 DC DG DC DG DC DG HET K A 101 1 HET 58I B 101 6 HETNAM K POTASSIUM ION HETNAM 58I 4-AZANIUMYLBUTYLAZANIUM HETSYN 58I BUTANE-1,4-DIYLDIAMMONIUM; PUTRESCINIUM FORMUL 3 K K 1+ FORMUL 4 58I C4 H14 N2 2+ FORMUL 5 HOH *123(H2 O) LINK OP1A DG A 6 K A K A 101 1555 1555 2.72 LINK O5'A DG A 6 K A K A 101 1555 1555 3.05 LINK K A K A 101 O HOH A 217 1555 1555 2.66 LINK K A K A 101 O AHOH A 248 1555 1555 2.61 LINK K A K A 101 OP1 DC B 9 3545 1555 3.18 LINK K A K A 101 OP2 DC B 9 3545 1555 2.79 LINK K A K A 101 O HOH B 255 1555 3555 3.39 CRYST1 17.970 31.020 43.860 90.00 90.00 90.00 P 21 21 21 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 0.055648 0.000000 0.000000 0.00000 SCALE2 0.000000 0.032237 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022800 0.00000