HEADER DNA 08-NOV-01 1KCI TITLE CRYSTAL STRUCTURE OF 9-AMINO-N-[2-(4-MORPHOLINYL)ETHYL]-4- TITLE 2 ACRIDINECARBOXAMIDE BOUND TO D(CGTACG)2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 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 DNA, INTERCALATOR, AMINOACRIDINECARBOXAMIDE EXPDTA X-RAY DIFFRACTION AUTHOR A.ADAMS,J.M.GUSS,W.A.DENNY,L.P.G.WAKELIN REVDAT 5 03-APR-24 1KCI 1 REMARK REVDAT 4 07-FEB-24 1KCI 1 REMARK REVDAT 3 24-FEB-09 1KCI 1 VERSN REVDAT 2 01-APR-03 1KCI 1 JRNL REVDAT 1 01-FEB-02 1KCI 0 JRNL AUTH A.ADAMS,J.M.GUSS,W.A.DENNY,L.P.WAKELIN JRNL TITL CRYSTAL STRUCTURE OF JRNL TITL 2 9-AMINO-N-[2-(4-MORPHOLINYL)ETHYL]-4-ACRIDINECARBOXAMIDE JRNL TITL 3 BOUND TO D(CGTACG)2: IMPLICATIONS FOR STRUCTURE-ACTIVITY JRNL TITL 4 RELATIONSHIPS OF ACRIDINECARBOXAMIDE TOPOISOMERASE POISONS. JRNL REF NUCLEIC ACIDS RES. V. 30 719 2002 JRNL REFN ISSN 0305-1048 JRNL PMID 11809884 JRNL DOI 10.1093/NAR/30.3.719 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : RFREE 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) : 0.219 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.215 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.291 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 143 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 1931 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL 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 : 52 REMARK 3 SOLVENT ATOMS : 20 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL 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: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : SHELX 2000 DNA DICTIOARY REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KCI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014810. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-00 REMARK 200 TEMPERATURE (KELVIN) : 110 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 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 : 1951 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : 21.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.35000 REMARK 200 FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ISOMORPHOUS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NDB ENTRY DD0015 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CACODYLATE, SPERMINE, KCL, MGCL2, MPD, REMARK 280 PH 6.0, VAPOR DIFFUSION, SITTING DROP, 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 13.11333 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 26.22667 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 13.11333 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 26.22667 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 30.23900 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 A4009 LIES ON A SPECIAL POSITION. REMARK 375 HOH A4019 LIES ON A SPECIAL POSITION. REMARK 375 HOH A4020 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 C2' DC A1001 C1' 0.119 REMARK 500 DC A1001 O4' DC A1001 C1' 0.077 REMARK 500 DC A1001 O3' DC A1001 C3' -0.054 REMARK 500 DC A1001 O3' DG A1002 P 0.113 REMARK 500 DG A1002 P DG A1002 O5' 0.075 REMARK 500 DG A1002 C2' DG A1002 C1' 0.126 REMARK 500 DG A1002 O3' DG A1002 C3' -0.062 REMARK 500 DG A1002 O3' DT A1003 P 0.118 REMARK 500 DT A1003 P DT A1003 O5' 0.073 REMARK 500 DT A1003 C2' DT A1003 C1' 0.142 REMARK 500 DT A1003 O3' DT A1003 C3' -0.070 REMARK 500 DT A1003 O3' DA A1004 P 0.110 REMARK 500 DA A1004 P DA A1004 O5' 0.080 REMARK 500 DA A1004 C2' DA A1004 C1' 0.122 REMARK 500 DA A1004 O3' DA A1004 C3' -0.057 REMARK 500 DA A1004 O3' DC A1005 P 0.132 REMARK 500 DC A1005 P DC A1005 O5' 0.067 REMARK 500 DC A1005 C2' DC A1005 C1' 0.140 REMARK 500 DC A1005 O3' DC A1005 C3' -0.052 REMARK 500 DC A1005 O3' DG A1006 P 0.130 REMARK 500 DG A1006 P DG A1006 O5' 0.067 REMARK 500 DG A1006 C2' DG A1006 C1' 0.128 REMARK 500 DG A1006 O3' DG A1006 C3' -0.056 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 O5' - C5' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 DC A1001 C5' - C4' - O4' ANGL. DEV. = 7.9 DEGREES REMARK 500 DC A1001 C4' - C3' - C2' ANGL. DEV. = 9.4 DEGREES REMARK 500 DC A1001 C3' - C2' - C1' ANGL. DEV. = -6.9 DEGREES REMARK 500 DC A1001 O4' - C1' - C2' ANGL. DEV. = 4.8 DEGREES REMARK 500 DC A1001 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG A1002 O5' - C5' - C4' ANGL. DEV. = -9.9 DEGREES REMARK 500 DG A1002 P - O5' - C5' ANGL. DEV. = -11.7 DEGREES REMARK 500 DG A1002 C5' - C4' - O4' ANGL. DEV. = 9.3 DEGREES REMARK 500 DG A1002 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 DG A1002 C3' - C2' - C1' ANGL. DEV. = -6.5 DEGREES REMARK 500 DG A1002 O4' - C1' - C2' ANGL. DEV. = 4.0 DEGREES REMARK 500 DT A1003 O5' - C5' - C4' ANGL. DEV. = -10.8 DEGREES REMARK 500 DT A1003 P - O5' - C5' ANGL. DEV. = -15.0 DEGREES REMARK 500 DT A1003 C5' - C4' - O4' ANGL. DEV. = 7.0 DEGREES REMARK 500 DT A1003 C4' - C3' - C2' ANGL. DEV. = 7.0 DEGREES REMARK 500 DT A1003 C3' - C2' - C1' ANGL. DEV. = -11.2 DEGREES REMARK 500 DT A1003 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES REMARK 500 DT A1003 C3' - O3' - P ANGL. DEV. = 11.5 DEGREES REMARK 500 DA A1004 O5' - C5' - C4' ANGL. DEV. = -9.5 DEGREES REMARK 500 DA A1004 C5' - C4' - O4' ANGL. DEV. = 7.2 DEGREES REMARK 500 DA A1004 C4' - C3' - C2' ANGL. DEV. = 8.1 DEGREES REMARK 500 DA A1004 C3' - C2' - C1' ANGL. DEV. = -7.4 DEGREES REMARK 500 DA A1004 O4' - C1' - C2' ANGL. DEV. = 5.0 DEGREES REMARK 500 DC A1005 O5' - C5' - C4' ANGL. DEV. = -8.7 DEGREES REMARK 500 DC A1005 P - O5' - C5' ANGL. DEV. = -10.2 DEGREES REMARK 500 DC A1005 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES REMARK 500 DC A1005 C4' - C3' - C2' ANGL. DEV. = 8.1 DEGREES REMARK 500 DC A1005 C3' - C2' - C1' ANGL. DEV. = -9.8 DEGREES REMARK 500 DG A1006 O5' - C5' - C4' ANGL. DEV. = -9.2 DEGREES REMARK 500 DG A1006 P - O5' - C5' ANGL. DEV. = -15.4 DEGREES REMARK 500 DG A1006 C4' - C3' - C2' ANGL. DEV. = 7.3 DEGREES REMARK 500 DG A1006 C3' - C2' - C1' ANGL. DEV. = -8.3 DEGREES REMARK 500 DG A1006 O4' - C1' - C2' ANGL. DEV. = 6.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: DD0015 RELATED DB: NDB REMARK 900 5'-D(CPGPTPAPCPG)-3', 9-AMINO-[N-(2-DIMETHYLAMINO)ETHYL]ACRIDINE-4- REMARK 900 CARBOXAMIDE REMARK 900 RELATED ID: DD0023 RELATED DB: NDB REMARK 900 5'-D(CPGPTPAPCPG)-3', 5-F-9-AMINO-[N-(2-DIMETHYLAMINO)ETHYL] REMARK 900 ACRIDINE-4-CARBOXAMIDE REMARK 900 RELATED ID: DDF073 RELATED DB: NDB REMARK 900 5'-D(CG5BRUACG)-3', 6BR-9-AMINO-[N-(2-DIMETHYLAMINO)ETHYL]ACRIDINE- REMARK 900 4-CARBOXAMIDE DBREF 1KCI A 1001 1006 PDB 1KCI 1KCI 1001 1006 SEQRES 1 A 6 DC DG DT DA DC DG HET DRC A3014 26 HET DRC A3015 26 HETNAM DRC 9-AMINO-N-[2-(4-MORPHOLINYL)ETHYL]-4- HETNAM 2 DRC ACRIDINECARBOXAMIDE FORMUL 2 DRC 2(C20 H22 N4 O2) FORMUL 4 HOH *20(H2 O) SITE 1 AC1 9 DC A1001 DG A1002 DT A1003 DA A1004 SITE 2 AC1 9 DC A1005 DG A1006 DRC A3015 HOH A4016 SITE 3 AC1 9 HOH A4019 SITE 1 AC2 4 DC A1001 DG A1006 DRC A3014 HOH A4011 CRYST1 30.239 30.239 39.340 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 0.033070 0.019093 0.000000 0.00000 SCALE2 0.000000 0.038186 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025419 0.00000