4R15 - Header Asymmetric Unit

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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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