HEADER DNA 14-APR-99 465D TITLE STRUCTURE OF THE TOPOISOMERASE II POISON BOUND TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS TOPOISOMERASE II POISON, HEXANUCLEOTIDE, D(CGTACG)2, 9-AMINO-DACA, KEYWDS 2 DNA EXPDTA X-RAY DIFFRACTION AUTHOR A.ADAMS,J.M.GUSS,C.A.COLLYER,W.A.DENNY,L.P.WAKELIN REVDAT 6 03-APR-24 465D 1 REMARK REVDAT 5 27-DEC-23 465D 1 REMARK REVDAT 4 14-FEB-18 465D 1 REMARK REVDAT 3 24-FEB-09 465D 1 VERSN REVDAT 2 07-SEP-99 465D 3 HETATM REVDAT 1 25-AUG-99 465D 0 JRNL AUTH A.ADAMS,J.M.GUSS,C.A.COLLYER,W.A.DENNY,L.P.WAKELIN JRNL TITL CRYSTAL STRUCTURE OF THE TOPOISOMERASE II POISON JRNL TITL 2 9-AMINO-[N-(2-DIMETHYLAMINO)ETHYL]ACRIDINE-4-CARBOXAMIDE JRNL TITL 3 BOUND TO THE DNA HEXANUCLEOTIDE D(CGTACG)2. JRNL REF BIOCHEMISTRY V. 38 9221 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10413496 JRNL DOI 10.1021/BI990352M REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT 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) : 0.196 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.195 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 8.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 225 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 2705 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.195 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.192 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 8.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 219 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 2664 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 120 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 29 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 182.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 791 REMARK 3 NUMBER OF RESTRAINTS : 999 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.021 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.038 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.023 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER,J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 465D 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_1000001347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-97 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2763 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 24.70 REMARK 200 R MERGE (I) : 0.02900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 56.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.14200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ISOMORPHOUS REPLACEMENT REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: DDF073 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 MM DNA, 20 MM SODIUM CACODYLATE REMARK 280 BUFFER, PH 6.5, 4 MM MAGNESIUM ACETATE, 1 MM COBALT(II) CHLORIDE, REMARK 280 0.33 MM SPERMINE.4HCL, 1 MM 9-AMINO-[N-(2- DIMETHYLAMINO)ETHYL] REMARK 280 ACRIDINE-4-CARBOXAMIDE AND 9% MPD EQUILIBRATED AGAINST 1 ML OF A REMARK 280 SOLUTION OF 45% MPD IN WATER, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 13.23067 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 26.46133 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 0.00000 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 13.23067 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 26.46133 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 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 -1.000000 0.000000 0.000000 30.16100 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A4025 LIES ON A SPECIAL POSITION. REMARK 375 HOH A4029 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DC A1001 C4' DC A1001 C3' 0.080 REMARK 500 DC A1001 C2' DC A1001 C1' 0.064 REMARK 500 DC A1001 O4' DC A1001 C1' 0.121 REMARK 500 DG A1002 C4' DG A1002 C3' 0.092 REMARK 500 DG A1002 C2' DG A1002 C1' 0.082 REMARK 500 DG A1002 O4' DG A1002 C1' 0.101 REMARK 500 DG A1002 O3' DT A1003 P 0.073 REMARK 500 DT A1003 C5' DT A1003 C4' 0.052 REMARK 500 DT A1003 C4' DT A1003 C3' 0.088 REMARK 500 DT A1003 C2' DT A1003 C1' 0.091 REMARK 500 DT A1003 O4' DT A1003 C1' 0.123 REMARK 500 DA A1004 C4' DA A1004 C3' 0.067 REMARK 500 DA A1004 C2' DA A1004 C1' 0.068 REMARK 500 DA A1004 O4' DA A1004 C1' 0.120 REMARK 500 DC A1005 C4' DC A1005 C3' 0.086 REMARK 500 DC A1005 C2' DC A1005 C1' 0.085 REMARK 500 DC A1005 O4' DC A1005 C1' 0.071 REMARK 500 DG A1006 C5' DG A1006 C4' 0.048 REMARK 500 DG A1006 C4' DG A1006 C3' 0.090 REMARK 500 DG A1006 C2' DG A1006 C1' 0.079 REMARK 500 DG A1006 O4' DG A1006 C1' 0.092 REMARK 500 REMARK 500 REMARK: NULL 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 A1001 N1 - C1' - C2' ANGL. DEV. = 11.0 DEGREES REMARK 500 DG A1002 O5' - C5' - C4' ANGL. DEV. = -7.5 DEGREES REMARK 500 DG A1002 P - O5' - C5' ANGL. DEV. = -10.2 DEGREES REMARK 500 DG A1002 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 DG A1002 O4' - C1' - N9 ANGL. DEV. = -9.4 DEGREES REMARK 500 DG A1002 C6 - N1 - C2 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG A1002 C5 - C6 - O6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT A1003 O5' - C5' - C4' ANGL. DEV. = -9.9 DEGREES REMARK 500 DT A1003 O4' - C1' - C2' ANGL. DEV. = -8.9 DEGREES REMARK 500 DT A1003 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DA A1004 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA A1004 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 DA A1004 O4' - C1' - N9 ANGL. DEV. = -11.6 DEGREES REMARK 500 DC A1005 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 DC A1005 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 DC A1005 C6 - N1 - C2 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG A1006 O5' - C5' - C4' ANGL. DEV. = -8.3 DEGREES REMARK 500 DG A1006 P - O5' - C5' ANGL. DEV. = -10.9 DEGREES REMARK 500 DG A1006 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG A1006 O4' - C1' - N9 ANGL. DEV. = -8.1 DEGREES REMARK 500 DG A1006 N9 - C4 - C5 ANGL. DEV. = -2.4 DEGREES REMARK 500 DG A1006 C5 - C6 - O6 ANGL. DEV. = -5.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 9AD A 3014 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 9AD A 3015 DBREF 465D A 1001 1006 PDB 465D 465D 1001 1006 SEQRES 1 A 6 DC DG DT DA DC DG HET 9AD A3014 23 HET 9AD A3015 23 HETNAM 9AD 9-AMINO-(N-(2-DIMETHYLAMINO)ETHYL)ACRIDINE-4- HETNAM 2 9AD CARBOXAMIDE FORMUL 2 9AD 2(C18 H20 N4 O) FORMUL 4 HOH *29(H2 O) SITE 1 AC1 8 DC A1001 DG A1002 DA A1004 DC A1005 SITE 2 AC1 8 DG A1006 9AD A3015 HOH A4010 HOH A4024 SITE 1 AC2 5 DC A1001 DG A1006 9AD A3014 HOH A4012 SITE 2 AC2 5 HOH A4015 CRYST1 30.161 30.161 39.692 90.00 90.00 120.00 P 64 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 0.033155 0.019142 0.000000 0.00000 SCALE2 0.000000 0.038285 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025194 0.00000