HEADER DNA 26-JAN-04 1V9G TITLE NEUTRON CRYSTALLOGRAPHIC ANALYSIS OF THE Z-DNA HEXAMER CGCGCG COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*GP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: Z-DNA DUPLEX SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS Z-DNA, HYDROGEN, HYDRATION, H/D EXCHANGE, NEUTRON, DNA EXPDTA NEUTRON DIFFRACTION AUTHOR T.CHATAKE,I.TANAKA,N.NIIMURA REVDAT 9 25-OCT-23 1V9G 1 REMARK REVDAT 8 05-DEC-18 1V9G 1 REMARK REVDAT 7 28-NOV-18 1V9G 1 SOURCE REMARK REVDAT 6 20-JUN-18 1V9G 1 REMARK REVDAT 5 07-MAR-18 1V9G 1 REMARK REVDAT 4 21-AUG-13 1V9G 1 SITE REVDAT 3 13-JUL-11 1V9G 1 VERSN REVDAT 2 24-FEB-09 1V9G 1 VERSN REVDAT 1 26-JAN-05 1V9G 0 JRNL AUTH T.CHATAKE,I.TANAKA,H.UMINO,S.ARAI,N.NIIMURA JRNL TITL THE HYDRATION STRUCTURE OF A Z-DNA HEXAMERIC DUPLEX JRNL TITL 2 DETERMINED BY A NEUTRON DIFFRACTION TECHNIQUE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 61 1088 2005 JRNL REFN ISSN 0907-4449 JRNL PMID 16041074 JRNL DOI 10.1107/S0907444905015581 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 72.5 REMARK 3 NUMBER OF REFLECTIONS : 1821 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.500 REMARK 3 FREE R VALUE TEST SET COUNT : 163 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 56.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 206 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE : 0.4250 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 19 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL 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 : 14 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 3.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.28900 REMARK 3 B22 (A**2) : 1.58100 REMARK 3 B33 (A**2) : -2.87000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.29 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.37 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.830 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 0.430 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.820 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : BULK SOLVENT CORRECTION REMARK 3 KSOL : 0.06 REMARK 3 BSOL : 20.10 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1V9G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000006373. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 10-JUN-03 REMARK 230 TEMPERATURE (KELVIN) : 298.0 REMARK 230 PH : 7.00 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : 1G-A REMARK 230 WAVELENGTH OR RANGE (A) : 2.88 REMARK 230 MONOCHROMATOR : ELASTICALLY-BENT PERFECT SILICON REMARK 230 MONOCHROMATOR REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : DIFFRACTOMETER REMARK 230 DETECTOR MANUFACTURER : BIX-3M REMARK 230 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 230 DATA SCALING SOFTWARE : SCALEPACK REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 2627 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 230 RESOLUTION RANGE LOW (A) : 50.000 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 73.7 REMARK 230 DATA REDUNDANCY : 2.000 REMARK 230 R MERGE (I) : 0.12700 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 6.2000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 230 COMPLETENESS FOR SHELL (%) : 40.9 REMARK 230 DATA REDUNDANCY IN SHELL : 1.70 REMARK 230 R MERGE FOR SHELL (I) : 0.20800 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 3.500 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : CNS REMARK 230 STARTING MODEL: PDB ENTRY 1IOT REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 7.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, SODIUM CACODYLATE, MAGNESIUM REMARK 280 CHLORIDE, SPERMINE, PH 7.0, SMALL TUBES, TEMPERATURE 328K 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 9.23000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.59000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.38000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.59000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 9.23000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.38000 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 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPW A 13 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IOT RELATED DB: PDB REMARK 900 THE SAME Z-DNA COMPLEXED WITH SPERMINE IN H2O DBREF 1V9G A 1 6 PDB 1V9G 1V9G 1 6 DBREF 1V9G B 7 12 PDB 1V9G 1V9G 7 12 SEQRES 1 A 6 DC DG DC DG DC DG SEQRES 1 B 6 DC DG DC DG DC DG HET SPW A 13 44 HETNAM SPW N,N'-BIS(3-AMMONIOPROPYL)BUTANE-1,4-DIAMINIUM HETSYN SPW SPERMINE (FULLY DEUTERATED FORM) FORMUL 3 SPW C10 H20 N4 4+ FORMUL 4 DOD *44(D2 O) SITE 1 AC1 9 DG A 2 DC A 3 DG A 4 DG B 8 SITE 2 AC1 9 DOD A 106 DOD B 119 DOD A 132 DOD A 135 SITE 3 AC1 9 DOD B 136 CRYST1 18.460 30.760 43.180 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 0.054171 0.000000 0.000000 0.00000 SCALE2 0.000000 0.032510 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023159 0.00000