HEADER DNA 12-SEP-00 1FTD TITLE 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'-SYMMETRIC BIS- TITLE 2 BENZIMIDAZOLE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS MINOR GROOVE BINDING, DNA EXPDTA X-RAY DIFFRACTION AUTHOR J.MANN,A.BARON,Y.OPOKU-BOAHEN,E.JOHANSSON,G.PARKINSON,L.R.KELLAND, AUTHOR 2 S.NEIDLE REVDAT 5 07-FEB-24 1FTD 1 REMARK LINK REVDAT 4 04-OCT-17 1FTD 1 REMARK REVDAT 3 24-FEB-09 1FTD 1 VERSN REVDAT 2 01-APR-03 1FTD 1 JRNL REVDAT 1 26-FEB-01 1FTD 0 JRNL AUTH J.MANN,A.BARON,Y.OPOKU-BOAHEN,E.JOHANSSON,G.PARKINSON, JRNL AUTH 2 L.R.KELLAND,S.NEIDLE JRNL TITL A NEW CLASS OF SYMMETRIC BISBENZIMIDAZOLE-BASED DNA MINOR JRNL TITL 2 GROOVE-BINDING AGENTS SHOWING ANTITUMOR ACTIVITY. JRNL REF J.MED.CHEM. V. 44 138 2001 JRNL REFN ISSN 0022-2623 JRNL PMID 11170623 JRNL DOI 10.1021/JM000297B REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM 10% REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.249 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.242 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 448 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 4198 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 : 486 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 85 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 : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FTD 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_1000011883. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 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 : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4427 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 1.100 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.10000 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: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, MPD, SPERMINE REMARK 280 TETRAHYDROCHLORIDE, NACL, MGCL2, PH 6.8, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 284K 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 12.57500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.82500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.97000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.82500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.57500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.97000 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 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 DA A 5 C1' DA A 5 N9 0.099 REMARK 500 DA A 6 C1' DA A 6 N9 0.112 REMARK 500 DA B 17 C1' DA B 17 N9 0.112 REMARK 500 DA B 18 C1' DA B 18 N9 0.107 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 A 1 O4' - C1' - N1 ANGL. DEV. = -7.2 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = -7.0 DEGREES REMARK 500 DA A 5 N9 - C1' - C2' ANGL. DEV. = 8.7 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = -4.7 DEGREES REMARK 500 DA A 6 N9 - C1' - C2' ANGL. DEV. = 8.9 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT A 7 N1 - C1' - C2' ANGL. DEV. = 9.9 DEGREES REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = -7.5 DEGREES REMARK 500 DT A 8 N1 - C1' - C2' ANGL. DEV. = 9.7 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = -8.5 DEGREES REMARK 500 DC A 9 N1 - C1' - C2' ANGL. DEV. = 8.8 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = -9.2 DEGREES REMARK 500 DC A 9 N1 - C2 - O2 ANGL. DEV. = 5.0 DEGREES REMARK 500 DC A 9 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 DC A 11 N1 - C1' - C2' ANGL. DEV. = 9.0 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = -7.6 DEGREES REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = -5.4 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = -7.3 DEGREES REMARK 500 DA B 17 N9 - C1' - C2' ANGL. DEV. = 8.6 DEGREES REMARK 500 DA B 17 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DA B 18 N9 - C1' - C2' ANGL. DEV. = 10.7 DEGREES REMARK 500 DA B 18 O4' - C1' - N9 ANGL. DEV. = -6.0 DEGREES REMARK 500 DT B 19 N1 - C1' - C2' ANGL. DEV. = 10.4 DEGREES REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = -8.9 DEGREES REMARK 500 DT B 20 N1 - C1' - C2' ANGL. DEV. = 9.1 DEGREES REMARK 500 DT B 20 O4' - C1' - N1 ANGL. DEV. = -7.3 DEGREES REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = -6.6 DEGREES REMARK 500 DC B 23 O4' - C1' - N1 ANGL. DEV. = -6.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 26 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 139 O REMARK 620 2 HOH A 140 O 90.2 REMARK 620 3 HOH A 141 O 178.9 90.8 REMARK 620 4 HOH A 142 O 88.6 178.6 90.4 REMARK 620 5 HOH A 143 O 90.1 88.1 90.5 91.2 REMARK 620 6 HOH A 144 O 89.7 90.0 89.7 90.7 178.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 26 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE E97 A 25 DBREF 1FTD A 1 12 PDB 1FTD 1FTD 1 12 DBREF 1FTD B 13 24 PDB 1FTD 1FTD 13 24 SEQRES 1 A 12 DC DG DC DG DA DA DT DT DC DG DC DG SEQRES 1 B 12 DC DG DC DG DA DA DT DT DC DG DC DG HET MG A 26 1 HET E97 A 25 44 HETNAM MG MAGNESIUM ION HETNAM E97 [3-(4-{2'-[4-(3-DIMETHYLAMINO-PROPOXY)-PHENYL]-3H,3'H- HETNAM 2 E97 [5,5']BIBENZOIMIDAZOLYL-2-YL}-PHENOXY)-PROPYL]- HETNAM 3 E97 DIMETHYL-AMINE FORMUL 3 MG MG 2+ FORMUL 4 E97 C36 H40 N6 O2 FORMUL 5 HOH *85(H2 O) LINK MG MG A 26 O HOH A 139 1555 1555 2.02 LINK MG MG A 26 O HOH A 140 1555 1555 2.02 LINK MG MG A 26 O HOH A 141 1555 1555 2.01 LINK MG MG A 26 O HOH A 142 1555 1555 2.01 LINK MG MG A 26 O HOH A 143 1555 1555 2.02 LINK MG MG A 26 O HOH A 144 1555 1555 2.02 SITE 1 AC1 6 HOH A 139 HOH A 140 HOH A 141 HOH A 142 SITE 2 AC1 6 HOH A 143 HOH A 144 SITE 1 AC2 17 DG A 4 DA A 6 DT A 7 DT A 8 SITE 2 AC2 17 DC A 9 DG A 10 DC A 11 DG A 12 SITE 3 AC2 17 DG B 16 DA B 17 DA B 18 DT B 19 SITE 4 AC2 17 DT B 20 DC B 21 DG B 22 DC B 23 SITE 5 AC2 17 DG B 24 CRYST1 25.150 39.940 65.650 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 0.039769 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025035 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015233 0.00000