HEADER DNA 21-JUN-00 1F6C TITLE CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH SPERMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*CP*GP*CP*C)-3'); COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS B-DNA, E-DNA, DOUBLE HELIX, DNA EXPDTA X-RAY DIFFRACTION AUTHOR J.M.VARGASON,B.F.EICHMAN,P.S.HO REVDAT 4 07-FEB-24 1F6C 1 REMARK LINK REVDAT 3 24-FEB-09 1F6C 1 VERSN REVDAT 2 28-SEP-00 1F6C 1 JRNL REVDAT 1 28-AUG-00 1F6C 0 JRNL AUTH J.M.VARGASON,B.F.EICHMAN,P.S.HO JRNL TITL THE EXTENDED AND ECCENTRIC E-DNA STRUCTURE INDUCED BY JRNL TITL 2 CYTOSINE METHYLATION OR BROMINATION. JRNL REF NAT.STRUCT.BIOL. V. 7 758 2000 JRNL REFN ISSN 1072-8368 JRNL PMID 10966645 JRNL DOI 10.1038/78985 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 4304 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) : 0.226 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.400 REMARK 3 FREE R VALUE TEST SET COUNT : 447 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 600 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -9.90240 REMARK 3 B22 (A**2) : -9.90240 REMARK 3 B33 (A**2) : 19.80480 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 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: ANISOTROPIC B VALUES WERE APPLIED TO REMARK 3 FCALC DURING REFINEMENT IN ORDER TO SCALE FCALC TO FOBS REMARK 4 REMARK 4 1F6C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000011297. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-98 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 6.0 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 : RIGAKU RU300 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 : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4526 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 500.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.39500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MGCL2, SPERMINE, SODIUM CACODYLATE, PH REMARK 280 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.81500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.75000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 14.90750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.75000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.75000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.72250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.75000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.75000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 14.90750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.75000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.75000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 44.72250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 29.81500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 59.63000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E 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 SPM D 31 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPM B 32 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F69 RELATED DB: PDB REMARK 900 B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE REMARK 900 RELATED ID: 1F6E RELATED DB: PDB REMARK 900 A-DNA HEXAMER GGCGM5CC REMARK 900 RELATED ID: 1F6I RELATED DB: PDB REMARK 900 E-DNA HEXAMER GGCGM5CC REMARK 900 RELATED ID: 1F6J RELATED DB: PDB REMARK 900 E-DNA HEXAMER GGCGBR5CC DBREF 1F6C A 1 6 PDB 1F6C 1F6C 1 6 DBREF 1F6C B 7 12 PDB 1F6C 1F6C 7 12 DBREF 1F6C C 13 18 PDB 1F6C 1F6C 13 18 DBREF 1F6C D 19 24 PDB 1F6C 1F6C 19 24 DBREF 1F6C E 25 30 PDB 1F6C 1F6C 25 30 SEQRES 1 A 6 DG DG DC DG DC DC SEQRES 1 B 6 DG DG DC DG DC DC SEQRES 1 C 6 DG DG DC DG DC DC SEQRES 1 D 6 DG DG DC DG DC DC SEQRES 1 E 6 DG DG DC DG DC DC HET SPM B 32 7 HET SPM D 31 14 HETNAM SPM SPERMINE FORMUL 6 SPM 2(C10 H26 N4) FORMUL 8 HOH *16(H2 O) LINK C7 SPM B 32 C7 SPM B 32 1555 7466 1.57 SITE 1 AC1 10 DG A 1 DG A 2 DC A 3 DG A 4 SITE 2 AC1 10 HOH A 34 DG B 7 DG B 8 DG D 19 SITE 3 AC1 10 DC E 29 DC E 30 SITE 1 AC2 7 DC A 3 DG A 4 DG B 7 DG B 8 SITE 2 AC2 7 DC B 9 HOH B 44 DG C 16 CRYST1 71.500 71.500 59.630 90.00 90.00 90.00 P 41 21 2 40 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 0.013986 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013986 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016770 0.00000