HEADER DNA 22-JAN-15 4XSN TITLE COPPER(II) BOUND TO THE Z-DNA FORM OF D(CGCGCG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*(BGM)P*CP*GP*CP*GP)-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, COPPER(II), DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.ROHNER,A.MEDINA-MOLNER,B.SPINGLER REVDAT 3 13-SEP-17 4XSN 1 REMARK REVDAT 2 13-JUL-16 4XSN 1 JRNL REVDAT 1 03-FEB-16 4XSN 0 JRNL AUTH M.ROHNER,A.MEDINA-MOLNER,B.SPINGLER JRNL TITL N,N,O AND N,O,N MERIDIONAL CIS COORDINATION OF TWO GUANINES JRNL TITL 2 TO COPPER(II) BY D(CGCGCG)2. JRNL REF INORG.CHEM. V. 55 6130 2016 JRNL REFN ISSN 0020-1669 JRNL PMID 27266259 JRNL DOI 10.1021/ACS.INORGCHEM.6B00672 REMARK 2 REMARK 2 RESOLUTION. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 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) : 0.121 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.120 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 4.937 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 378 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 7657 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.107 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.106 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.143 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 4.975 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 309 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 6211 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 242 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 98 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 341.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2609 REMARK 3 NUMBER OF RESTRAINTS : 5420 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.367 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.003 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.040 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.019 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.009 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.022 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY ? REMARK 4 REMARK 4 4XSN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000206001. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 183 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : STOE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-AREA REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7657 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.452 REMARK 200 RESOLUTION RANGE LOW (A) : 17.359 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : 0.05260 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.32640 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CACODYLATE, MPD, CALCIUM LACTATE, REMARK 280 POTASSIUM CHLORIDE, PH 7, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 296K 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 9.39950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.63900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.53850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.63900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 9.39950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 14.53850 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: 1830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 DC A 3 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 DC A 3 C5 - C6 - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC A 3 N3 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG A 4 O5' - C5' - C4' ANGL. DEV. = -6.9 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 DC A 5 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 DC B 1 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC B 1 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 DG B 4 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 DG B 4 C4 - C5 - C6 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG B 4 N3 - C4 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG B 4 C6 - C5 - N7 ANGL. DEV. = -5.1 DEGREES REMARK 500 DG B 4 N1 - C6 - O6 ANGL. DEV. = 6.3 DEGREES REMARK 500 DG B 4 C5 - C6 - O6 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC B 5 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC B 5 N3 - C4 - C5 ANGL. DEV. = -2.9 DEGREES REMARK 500 DG B 6 O4' - C1' - N9 ANGL. DEV. = -4.2 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 CU B 101 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 6 N7 REMARK 620 2 HOH B 213 O 88.2 REMARK 620 3 HOH B 208 O 103.7 89.9 REMARK 620 4 DG B 4 N7 97.5 36.9 53.0 REMARK 620 5 DG B 4 O6 84.9 40.5 52.1 13.4 REMARK 620 6 HOH B 211 O 93.5 178.2 89.4 142.4 139.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XQY RELATED DB: PDB REMARK 900 RELATED ID: 4XQZ RELATED DB: PDB DBREF 4XSN A 1 6 PDB 4XSN 4XSN 1 6 DBREF 4XSN B 1 6 PDB 4XSN 4XSN 1 6 SEQRES 1 A 6 DC BGM DC DG DC DG SEQRES 1 B 6 DC BGM DC DG DC DG HET BGM A 2 23 HET BGM B 2 23 HET CU B 101 1 HETNAM BGM 8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE HETNAM CU COPPER (II) ION FORMUL 1 BGM 2(C10 H13 BR N5 O7 P) FORMUL 3 CU CU 2+ FORMUL 4 HOH *98(H2 O) LINK O3' DC A 1 P BGM A 2 1555 1555 1.61 LINK O3' BGM A 2 P DC A 3 1555 1555 1.61 LINK O3' DC B 1 P BGM B 2 1555 1555 1.57 LINK O3' BGM B 2 P B DC B 3 1555 1555 1.59 LINK O3' BGM B 2 P A DC B 3 1555 1555 1.60 LINK N7 DG B 6 CU CU B 101 1555 1555 2.01 LINK CU CU B 101 O HOH B 213 1555 1555 2.07 LINK CU CU B 101 O HOH B 208 1555 1555 2.37 LINK N7 DG B 4 CU CU B 101 1555 4566 2.57 LINK O6 DG B 4 CU CU B 101 1555 4566 2.01 LINK CU CU B 101 O HOH B 211 1555 4466 1.95 SITE 1 AC1 5 DG B 4 DG B 6 HOH B 208 HOH B 211 SITE 2 AC1 5 HOH B 213 CRYST1 18.799 29.077 43.278 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 0.053194 0.000000 0.000000 0.00000 SCALE2 0.000000 0.034391 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023106 0.00000