HEADER DNA 04-AUG-14 4R15 TITLE HIGH-RESOLUTION CRYSTAL STRUCTURE OF Z-DNA IN COMPLEX WITH CR3+ TITLE 2 CATIONS 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 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 22-APR-15 4R15 1 JRNL REVDAT 1 04-MAR-15 4R15 0 JRNL AUTH P.DROZDZAL,M.GILSKI,R.KIERZEK,L.LOMOZIK,M.JASKOLSKI JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURE OF Z-DNA IN COMPLEX WITH JRNL TITL 2 CR(3+) CATIONS. JRNL REF J.BIOL.INORG.CHEM. V. 20 595 2015 JRNL REFN ISSN 0949-8257 JRNL PMID 25687556 JRNL DOI 10.1007/S00775-015-1247-5 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.DROZDZAL,M.GILSKI,R.KIERZEK,L.LOMOZIK,M.JASKOLSKI REMARK 1 TITL ULTRAHIGH-RESOLUTION CRYSTAL STRUCTURES OF Z-DNA IN COMPLEX REMARK 1 TITL 2 WITH MN(2+) AND ZN(2+) IONS. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 69 1180 2013 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 23695262 REMARK 1 DOI 10.1107/S0907444913007798 REMARK 1 REFERENCE 2 REMARK 1 AUTH Z.LUO,M.DAUTER,Z.DAUTER REMARK 1 TITL PHOSPHATES IN THE Z-DNA DODECAMER ARE FLEXIBLE, BUT THEIR REMARK 1 TITL 2 P-SAD SIGNAL IS SUFFICIENT FOR STRUCTURE SOLUTION. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 70 1790 2014 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 25004957 REMARK 1 DOI 10.1107/S1399004714004684 REMARK 1 REFERENCE 3 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 PMID 21459852 REMARK 1 DOI 10.1093/NAR/GKR202 REMARK 2 REMARK 2 RESOLUTION. 0.97 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) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 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) : 0.145 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.144 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1858 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 26535 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.133 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.132 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 6.930 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1459 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 21571 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 : 3 REMARK 3 SOLVENT ATOMS : 67 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 280.78 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 136.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 13 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 3347 REMARK 3 NUMBER OF RESTRAINTS : 6729 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.038 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) : 0.029 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.009 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.065 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.096 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 : CLOWNEY, GELBIN & PARKINSON REMARK 3 SPECIAL CASE: PHOSPHATE AND GLYCOSIDIC ANGLES ACCORDING TO PDB REMARK 3 MODEL 3P4J REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE REFINEMENT WAS CARRIED OUT AGAINST REMARK 3 SEPARATE BIJVOET PAIRS. ANISOTROPIC ATOMIC DISPLACEMENT REMARK 3 PARAMETERS WERE USED. ANISOTROPIC REFINEMENT REDUCED FREE R- REMARK 3 FACTOR FROM 0.2585 TO 0.1976. HYDROGEN ATOMS WERE ADDED AT RIDING REMARK 3 POSITION THE FINAL REFINEMENT WAS CALCULATED USING WEIGHTED FULL- REMARK 3 MATRIX LEAST-SQUARES PROCEDURE AND ALL REFLECTIONS. REMARK 4 REMARK 4 4R15 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-AUG-14. REMARK 100 THE RCSB ID CODE IS RCSB086768. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26535 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.970 REMARK 200 RESOLUTION RANGE LOW (A) : 24.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 2.530 REMARK 200 R MERGE (I) : 0.01600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.8500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.14 REMARK 200 R MERGE FOR SHELL (I) : 0.43200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.050 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: PDB ENTRY 4HIF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 24.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: A 1.5 MM WATER SOLUTION OF DNA MIXED REMARK 280 1:1 V/V WITH 10% MPD, 12 MM SPERMINE*4HCL, 12 MM NACL, 80 MM KCL REMARK 280 AND EQUILIBRATED AGAINST 35% MPD, PH 6. FOR CR3+ SOAKING, THE REMARK 280 CRYSTAL WAS PLACED FOR SEVERAL DAYS IN 0.002 ML OF THE RESERVOIR REMARK 280 SOLUTION MIXED WITH 0.002 ML OF 5 MM [CR(H2O)6]CL3, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 292.0K 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 9.07000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.47000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.22000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.47000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 9.07000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.22000 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 300 REMARK: SELF-COMPLEMENTARY DIMER OF CHAINS A AND B 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: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 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 DG A 4 O4' - C1' - C2' ANGL. DEV. = 3.4 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 HOH A 216 O REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CR A 101 CR REMARK 620 2 CR B 101 CR 67.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HOH A 201 O REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CR A 101 CR REMARK 620 2 CR B 101 CR 64.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CR A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CR A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CR B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HIF RELATED DB: PDB REMARK 900 RELATED ID: 4HIG RELATED DB: PDB REMARK 900 RELATED ID: 4OCB RELATED DB: PDB REMARK 900 RELATED ID: 3WBO RELATED DB: PDB REMARK 900 RELATED ID: 2HTO RELATED DB: PDB REMARK 900 RELATED ID: 1OMK RELATED DB: PDB REMARK 900 RELATED ID: 3P4J RELATED DB: PDB DBREF 4R15 A 1 6 PDB 4R15 4R15 1 6 DBREF 4R15 B 7 12 PDB 4R15 4R15 7 12 SEQRES 1 A 6 DC DG DC DG DC DG SEQRES 1 B 6 DC DG DC DG DC DG HET CR A 101 1 HET CR A 102 1 HET CR B 101 1 HETNAM CR CHROMIUM ION FORMUL 3 CR 3(CR 3+) FORMUL 6 HOH *67(H2 O) LINK CR CR A 101 O HOH A 215 1555 1555 1.73 LINK CR CR A 101 O HOH A 216 1555 1555 1.79 LINK CR CR A 102 O BHOH A 219 1555 1555 1.83 LINK CR CR A 101 O AHOH A 201 1555 1555 1.89 LINK CR CR A 102 O HOH A 236 1555 1555 1.90 LINK CR CR B 101 O BHOH A 201 1555 1555 1.95 LINK CR CR A 102 O HOH A 218 1555 1555 1.95 LINK CR CR B 101 O HOH B 212 1555 1555 1.95 LINK CR CR B 101 O HOH B 204 1555 1555 2.00 LINK CR CR A 101 O HOH A 238 1555 1555 2.03 LINK CR CR B 101 O HOH B 220 1555 1555 2.03 LINK CR CR A 101 O HOH A 212 1555 1555 2.06 LINK CR CR A 102 O HOH A 224 1555 1555 2.06 LINK CR CR B 101 O HOH A 216 1555 1555 2.35 LINK CR CR A 101 O HOH A 221 1555 1555 2.41 LINK CR CR B 101 O AHOH A 201 1555 1555 2.42 LINK CR CR A 102 O HOH A 220 1555 1555 2.43 LINK CR CR A 102 O AHOH A 219 1555 1555 2.65 SITE 1 AC1 7 HOH A 201 HOH A 212 HOH A 215 HOH A 216 SITE 2 AC1 7 HOH A 221 HOH A 238 CR B 101 SITE 1 AC2 5 HOH A 218 HOH A 219 HOH A 220 HOH A 224 SITE 2 AC2 5 HOH A 236 SITE 1 AC3 8 CR A 101 HOH A 201 HOH A 215 HOH A 216 SITE 2 AC3 8 HOH A 238 HOH B 204 HOH B 212 HOH B 220 CRYST1 18.140 30.440 42.940 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 0.055127 0.000000 0.000000 0.00000 SCALE2 0.000000 0.032852 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023288 0.00000 MASTER 276 0 3 0 0 0 6 6 0 0 0 2 END