HEADER DNA 07-JUN-18 6A1O TITLE CRYSTAL STRUCTURES OF DISORDERED Z-TYPE HELICES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*TP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*CP*A)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(P*TP*GP*TP*G)-3'); COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA (5'-D(P*CP*AP*CP*A)-3'); COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 4; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS DECAMERIC SEQUENCE, LEFT HANDED Z-DNA DUPLEX, DISCONTINUOUS HELICES, KEYWDS 2 HEXAGONAL SPACE GROUP, DNA EXPDTA X-RAY DIFFRACTION AUTHOR S.KARTHIK,P.K.MANDAL,A.THIRUGNANASAMBANDAM,N.GAUTHAM REVDAT 4 22-NOV-23 6A1O 1 REMARK REVDAT 3 22-MAY-19 6A1O 1 JRNL REVDAT 2 30-JAN-19 6A1O 1 JRNL REVDAT 1 16-JAN-19 6A1O 0 JRNL AUTH S.KARTHIK,P.K.MANDAL,A.THIRUGNANASAMBANDAM,N.GAUTHAM JRNL TITL CRYSTAL STRUCTURES OF DISORDERED Z-TYPE HELICES. JRNL REF NUCLEOSIDES NUCLEOTIDES V. 38 279 2019 JRNL REF 2 NUCLEIC ACIDS JRNL REFN ISSN 1525-7770 JRNL PMID 30588873 JRNL DOI 10.1080/15257770.2018.1517883 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1-2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 1584 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.275 REMARK 3 R VALUE (WORKING SET) : 0.280 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.160 REMARK 3 FREE R VALUE TEST SET COUNT : 161 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 14.6302 - 2.5068 0.87 1394 160 0.2722 0.2882 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: 0.5100 REMARK 3 OPERATOR: H,-H-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 272 REMARK 3 ANGLE : 1.236 410 REMARK 3 CHIRALITY : 0.089 48 REMARK 3 PLANARITY : 0.005 12 REMARK 3 DIHEDRAL : 33.515 108 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 2 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4989 30.7529 -21.6086 REMARK 3 T TENSOR REMARK 3 T11: 0.2704 T22: 0.3360 REMARK 3 T33: -0.0857 T12: 0.1189 REMARK 3 T13: -0.0807 T23: -0.2087 REMARK 3 L TENSOR REMARK 3 L11: 0.0470 L22: 0.0014 REMARK 3 L33: 0.0105 L12: -0.0097 REMARK 3 L13: 0.0194 L23: -0.0046 REMARK 3 S TENSOR REMARK 3 S11: -0.0112 S12: -0.0016 S13: 0.0205 REMARK 3 S21: 0.0096 S22: -0.0264 S23: 0.0305 REMARK 3 S31: -0.0350 S32: -0.0253 S33: -0.0226 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 3 THROUGH 4 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.6175 26.0683 -22.8904 REMARK 3 T TENSOR REMARK 3 T11: 0.0714 T22: 0.2822 REMARK 3 T33: 0.2987 T12: 0.0354 REMARK 3 T13: 0.1687 T23: -0.1321 REMARK 3 L TENSOR REMARK 3 L11: 0.0588 L22: 0.0878 REMARK 3 L33: 0.0766 L12: 0.0144 REMARK 3 L13: 0.0669 L23: 0.0264 REMARK 3 S TENSOR REMARK 3 S11: -0.0149 S12: -0.0020 S13: 0.0026 REMARK 3 S21: -0.0090 S22: -0.0113 S23: -0.0146 REMARK 3 S31: -0.0016 S32: 0.0422 S33: -0.0184 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 5 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.9363 40.2699 -18.6792 REMARK 3 T TENSOR REMARK 3 T11: 0.0654 T22: 0.0843 REMARK 3 T33: -0.0223 T12: 0.0214 REMARK 3 T13: -0.0940 T23: -0.0571 REMARK 3 L TENSOR REMARK 3 L11: 0.0044 L22: 0.0090 REMARK 3 L33: 0.0603 L12: 0.0051 REMARK 3 L13: 0.0139 L23: 0.0244 REMARK 3 S TENSOR REMARK 3 S11: -0.0115 S12: -0.0211 S13: 0.0029 REMARK 3 S21: 0.0070 S22: -0.0357 S23: 0.0036 REMARK 3 S31: -0.0335 S32: 0.0114 S33: -0.0281 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 9 THROUGH 12 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.0649 32.8064 -20.0410 REMARK 3 T TENSOR REMARK 3 T11: 0.0758 T22: 0.1437 REMARK 3 T33: -0.2564 T12: 0.0033 REMARK 3 T13: 0.1559 T23: -0.0454 REMARK 3 L TENSOR REMARK 3 L11: 0.0092 L22: 0.0372 REMARK 3 L33: 0.0068 L12: 0.0033 REMARK 3 L13: 0.0086 L23: 0.0049 REMARK 3 S TENSOR REMARK 3 S11: -0.0039 S12: 0.0239 S13: -0.0071 REMARK 3 S21: -0.0018 S22: -0.0240 S23: -0.0170 REMARK 3 S31: 0.0204 S32: 0.0350 S33: -0.0231 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6A1O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1300008020. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS GPLV2 REMARK 200 DATA SCALING SOFTWARE : XDS GPLV2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1584 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 16.816 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 4.384 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.17100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.240 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.6.0 REMARK 200 STARTING MODEL: 1D53 REMARK 200 REMARK 200 REMARK: AUTHORS STATE THAT THE PACKING REQUIREMENT IMPOSES REMARK 200 STATISTICAL DISORDER IN THE MOLECULE LEADING TO ONLY A PORTION REMARK 200 OF THE MOLECULE TO BE PRESENT IN ASYMMETRIC UNIT (ONE TETRAMER REMARK 200 AND A DINUCLEOTIDE STEP). HENCE THE TERMINAL PHOSPHATE ATOMS REMARK 200 APPEARS TO BE IN CLOSE CONTACT WITH THE SYMMETRY RELATED REMARK 200 TERMINAL OXYGENS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1MM DNA, 50MM SODIUM CACODYLATE REMARK 280 TRIHYDRATE BUFFER, 50MM CACL2, 50% MPD., PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.69600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 14.34800 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.52200 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 7.17400 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.87000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 P DC B 3 O3' DA B 4 6654 0.72 REMARK 500 P DT A 1 O3' DG A 2 5565 0.98 REMARK 500 OP2 DT A 1 O3' DG A 2 5565 1.46 REMARK 500 OP1 DC B 3 O3' DA B 4 6654 1.67 REMARK 500 P DC D 9 O3' DA D 12 2864 1.74 REMARK 500 O5' DC B 3 O3' DA B 4 6654 1.80 REMARK 500 OP1 DC D 9 O3' DA D 12 2864 1.92 REMARK 500 P DT C 5 O3' DG C 8 3785 2.05 REMARK 500 REMARK 500 REMARK: NULL DBREF 6A1O A 1 2 PDB 6A1O 6A1O 1 2 DBREF 6A1O B 3 4 PDB 6A1O 6A1O 3 4 DBREF 6A1O C 5 8 PDB 6A1O 6A1O 5 8 DBREF 6A1O D 9 12 PDB 6A1O 6A1O 9 12 SEQRES 1 A 2 DT DG SEQRES 1 B 2 DC DA SEQRES 1 C 4 DT DG DT DG SEQRES 1 D 4 DC DA DC DA FORMUL 5 HOH *3(H2 O) CRYST1 31.112 31.112 43.044 90.00 90.00 120.00 P 65 6 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 0.032142 0.018557 0.000000 0.00000 SCALE2 0.000000 0.037114 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023232 0.00000