HEADER DNA 11-OCT-12 4HIG TITLE ULTRAHIGH-RESOLUTION CRYSTAL STRUCTURE OF Z-DNA IN COMPLEX WITH MN2+ TITLE 2 ION. 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; SOURCE 5 OTHER_DETAILS: SYNTHETIC CONSTRUCT KEYWDS SELF-COMPLEMENTARY DNA, Z-DNA, DNA EXPDTA X-RAY DIFFRACTION AUTHOR P.DROZDZAL,M.GILSKI,R.KIERZEK,L.LOMOZIK,M.JASKOLSKI REVDAT 2 20-SEP-23 4HIG 1 REMARK LINK REVDAT 1 05-JUN-13 4HIG 0 JRNL AUTH P.DROZDZAL,M.GILSKI,R.KIERZEK,L.LOMOZIK,M.JASKOLSKI JRNL TITL ULTRAHIGH-RESOLUTION CRYSTAL STRUCTURES OF Z-DNA IN COMPLEX JRNL TITL 2 WITH MN(2+) AND ZN(2+) IONS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 1180 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 23695262 JRNL DOI 10.1107/S0907444913007798 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.BRZEZINSKI,A.BRZUSZKIEWICZ,M.DAUTER,M.KUBICKI,M.JASKOLSKI, REMARK 1 AUTH 2 Z.DAUTER REMARK 1 TITL HIGH REGULARITY OF Z-DNA REVEALED BY ULTRA HIGH-RESOLUTION REMARK 1 TITL 2 CRYSTAL STRUCTURE AT 0.55 A. REMARK 1 REF NUCLEIC ACIDS RES. V. 39 6238 2011 REMARK 1 REFN ISSN 0305-1048 REMARK 1 REFERENCE 2 REMARK 1 AUTH Z.DAUTER,D.A.ADAMIAK REMARK 1 TITL ANOMALOUS SIGNAL OF PHOSPHORUS USED FOR PHASING DNA REMARK 1 TITL 2 OLIGOMER: IMPORTANCE OF DATA REDUNDANCY. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 57 990 2001 REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 0.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 79.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R 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) : 0.071 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.071 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.081 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 2.110 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1009 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 47730 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.071 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.071 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.079 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 2.110 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1005 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 47641 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 : 15 REMARK 3 SOLVENT ATOMS : 92 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 332.97 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 164.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 3409 REMARK 3 NUMBER OF RESTRAINTS : 1139 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.000 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) : 0.028 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.037 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.069 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.(1975) 91, 201. 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. ANISOTROPIC ADPS. ANISOTROPIC REFINEMENT REMARK 3 REDUCED FREE R-FACTOR FROM 0.1295 TO 0.0903. HYDROGEN ATOMS WERE REMARK 3 ADDED AT RIDING POSITIONS. THE FINAL REFINEMENT WAS CALCULATED REMARK 3 USING WEIGHTED FULL MATRIX LEAST-SQUARES PROCEDURE. REMARK 4 REMARK 4 4HIG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075506. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-09; 16-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG; BESSY REMARK 200 BEAMLINE : X12; 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8010; 0.9184 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL; SI 111 CHANNEL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM; RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47730 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.750 REMARK 200 RESOLUTION RANGE LOW (A) : 25.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.9 REMARK 200 DATA REDUNDANCY : 3.280 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 10.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.15 REMARK 200 R MERGE FOR SHELL (I) : 0.03800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 11.39 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: 1I0T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 22.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 MM DNA WATER SOLUTION MIXED 1:1 REMARK 280 V/V WITH 10% MPD, 12 MM SPERMINE TETRA-HCL, 12 MM NACL, 80 MM REMARK 280 KCL AND EQUILIBRATED AGAINST 35% MPD, PH 6. VAPOR DIFFUSION, REMARK 280 HANGING DROP METHOD, TEMPERATURE 292K. FOR MN2+ SOAKING, A REMARK 280 CRYSTAL WAS PLACED IN 0.002 ML OF THE RESERVOIR SOLUTION MIXED REMARK 280 WITH 0.002 ML OF 5 MM MNCL2 FOR ONE WEEK. 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 8.86600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.96750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.71800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.96750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 8.86600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.71800 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: 940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 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 MN A 102 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 6 N7 REMARK 620 2 HOH A 203 O 91.6 REMARK 620 3 HOH A 203 O 86.8 8.4 REMARK 620 4 HOH A 216 O 92.1 96.9 103.9 REMARK 620 5 HOH A 216 O 87.0 69.7 76.3 27.9 REMARK 620 6 HOH A 250 O 92.5 148.2 155.4 51.5 79.1 REMARK 620 7 HOH A 250 O 84.6 174.3 171.0 79.1 105.8 28.4 REMARK 620 8 HOH A 251 O 175.9 92.4 97.0 88.4 95.4 84.6 91.5 REMARK 620 9 HOH A 252 O 93.8 92.2 85.6 169.0 161.9 118.9 92.3 85.0 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPK A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3G2R RELATED DB: PDB REMARK 900 RELATED ID: 3FQ5 RELATED DB: PDB REMARK 900 RELATED ID: 1ICK RELATED DB: PDB REMARK 900 RELATED ID: 1D39 RELATED DB: PDB REMARK 900 RELATED ID: 3P4J RELATED DB: PDB REMARK 900 RELATED ID: 4HIF RELATED DB: PDB DBREF 4HIG A 1 6 PDB 4HIG 4HIG 1 6 DBREF 4HIG B 7 12 PDB 4HIG 4HIG 7 12 SEQRES 1 A 6 DC DG DC DG DC DG SEQRES 1 B 6 DC DG DC DG DC DG HET SPK A 101 17 HET MN A 102 1 HETNAM SPK SPERMINE (FULLY PROTONATED FORM) HETNAM MN MANGANESE (II) ION FORMUL 3 SPK C10 H30 N4 4+ FORMUL 4 MN MN 2+ FORMUL 5 HOH *92(H2 O) LINK N7 DG A 6 MN MN A 102 1555 1555 2.26 LINK MN MN A 102 O AHOH A 203 1555 1555 2.08 LINK MN MN A 102 O BHOH A 203 1555 1555 2.31 LINK MN MN A 102 O AHOH A 216 1555 1555 2.19 LINK MN MN A 102 O BHOH A 216 1555 1555 2.26 LINK MN MN A 102 O BHOH A 250 1555 1555 1.95 LINK MN MN A 102 O AHOH A 250 1555 1555 2.21 LINK MN MN A 102 O HOH A 251 1555 1555 2.16 LINK MN MN A 102 O HOH A 252 1555 1555 2.14 SITE 1 AC1 15 DG A 2 DG A 4 DC A 5 DG A 6 SITE 2 AC1 15 HOH A 207 HOH A 214 HOH A 233 DC B 7 SITE 3 AC1 15 DG B 8 DC B 9 HOH B 111 HOH B 112 SITE 4 AC1 15 HOH B 113 HOH B 123 HOH B 126 SITE 1 AC2 6 DG A 6 HOH A 203 HOH A 216 HOH A 250 SITE 2 AC2 6 HOH A 251 HOH A 252 CRYST1 17.732 31.436 43.935 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 0.056395 0.000000 0.000000 0.00000 SCALE2 0.000000 0.031811 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022761 0.00000