HEADER DNA 16-JUL-02 1M6F TITLE STRONG BINDING IN THE DNA MINOR GROOVE BY AN AROMATIC DIAMIDINE WITH A TITLE 2 SHAPE THAT DOES NOT MATCH THE CURVATURE OF THE GROOVE 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 NUCLEIC ACIDS, MINOR GROOVE BINDER, DOUBLE HELIX, DNA-DRUG COMPLEX, KEYWDS 2 DNA EXPDTA X-RAY DIFFRACTION AUTHOR B.NGUYEN,M.P.H.LEE,D.HAMELBERG,A.JOUBERT,C.BAILLY,R.BRUN,S.NEIDLE, AUTHOR 2 W.D.WILSON REVDAT 5 03-APR-24 1M6F 1 REMARK REVDAT 4 14-FEB-24 1M6F 1 REMARK HETSYN LINK REVDAT 3 11-OCT-17 1M6F 1 REMARK REVDAT 2 24-FEB-09 1M6F 1 VERSN REVDAT 1 15-NOV-02 1M6F 0 JRNL AUTH B.NGUYEN,M.P.H.LEE,D.HAMELBERG,A.JOUBERT,C.BAILLY,R.BRUN, JRNL AUTH 2 S.NEIDLE,W.D.WILSON JRNL TITL STRONG BINDING IN THE DNA MINOR GROOVE BY AN AROMATIC JRNL TITL 2 DIAMIDINE WITH A SHAPE THAT DOES NOT MATCH THE CURVATURE OF JRNL TITL 3 THE GROOVE JRNL REF J.AM.CHEM.SOC. V. 124 13680 2002 JRNL REFN ISSN 0002-7863 JRNL PMID 12431090 JRNL DOI 10.1021/JA027953C REMARK 2 REMARK 2 RESOLUTION. 1.78 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) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL 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) : 0.205 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.202 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 298 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 5636 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.202 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.199 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 289 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 5477 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 : 27 REMARK 3 SOLVENT ATOMS : 117 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) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.020 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.019 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.006 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.010 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 : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1M6F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUL-02. REMARK 100 THE DEPOSITION ID IS D_1000016655. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 104 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 : YALE FOCUSSING MIRRORS 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 : 6040 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 17.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18400 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: X-PLOR REMARK 200 STARTING MODEL: DNA PART OF NDB ENTRY GDL009 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MGCL2 2UL OF 75MM, DNA DOUBLE-STRANDED REMARK 280 3UL OF 2MM, MPD 2UL OF 25%, DRUG 2UL OF 4.5MM, SODIUM CACODYLATE REMARK 280 40MM. MPD IN RESERVOIR 700UL OF 50%., PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 285K 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 12.04900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.81000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.91050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.81000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.04900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.91050 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 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 O4' - C1' - N1 ANGL. DEV. = -6.9 DEGREES REMARK 500 DG A1002 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DC A1003 O4' - C1' - N1 ANGL. DEV. = -5.4 DEGREES REMARK 500 DA A1005 O4' - C1' - N9 ANGL. DEV. = -7.9 DEGREES REMARK 500 DA A1006 O4' - C1' - N9 ANGL. DEV. = -8.5 DEGREES REMARK 500 DT A1007 N1 - C1' - C2' ANGL. DEV. = 9.7 DEGREES REMARK 500 DT A1007 O4' - C1' - N1 ANGL. DEV. = -9.3 DEGREES REMARK 500 DT A1008 N1 - C1' - C2' ANGL. DEV. = 8.8 DEGREES REMARK 500 DT A1008 O4' - C1' - N1 ANGL. DEV. = -8.0 DEGREES REMARK 500 DC A1009 O4' - C1' - N1 ANGL. DEV. = -6.0 DEGREES REMARK 500 DC A1011 O4' - C1' - N1 ANGL. DEV. = -9.0 DEGREES REMARK 500 DC B2015 O4' - C1' - N1 ANGL. DEV. = -7.2 DEGREES REMARK 500 DG B2016 O4' - C1' - N9 ANGL. DEV. = -4.6 DEGREES REMARK 500 DA B2017 O4' - C1' - N9 ANGL. DEV. = -11.2 DEGREES REMARK 500 DA B2018 N9 - C1' - C2' ANGL. DEV. = 9.3 DEGREES REMARK 500 DA B2018 O4' - C1' - N9 ANGL. DEV. = -12.1 DEGREES REMARK 500 DT B2019 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DT B2020 N1 - C1' - C2' ANGL. DEV. = 9.6 DEGREES REMARK 500 DT B2020 O4' - C1' - N1 ANGL. DEV. = -9.6 DEGREES REMARK 500 DT B2020 N3 - C4 - O4 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC B2021 N1 - C1' - C2' ANGL. DEV. = 8.5 DEGREES REMARK 500 DC B2021 O4' - C1' - N1 ANGL. DEV. = -11.3 DEGREES REMARK 500 DG B2022 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 DG B2024 O4' - C1' - N9 ANGL. DEV. = -4.3 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 A4026 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A8113 O REMARK 620 2 HOH A8114 O 88.7 REMARK 620 3 HOH A8115 O 176.6 88.7 REMARK 620 4 HOH A8116 O 90.6 90.5 91.5 REMARK 620 5 HOH A8117 O 90.9 91.4 87.1 177.6 REMARK 620 6 HOH B8112 O 91.0 179.6 91.7 89.6 88.5 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 CGQ B 3025 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 4026 DBREF 1M6F A 1001 1012 PDB 1M6F 1M6F 1001 1012 DBREF 1M6F B 2013 2024 PDB 1M6F 1M6F 2013 2024 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 A4026 1 HET CGQ B3025 35 HETNAM MG MAGNESIUM ION HETNAM CGQ 3-[C-[N'-(3-CARBAMIMIDOYL-BENZYLIDENIUM)-HYDRAZINO]- HETNAM 2 CGQ [[AMINOMETHYLIDENE]AMINIUM]-IMINOMETHYL]-BENZAMIDINIUM HETSYN CGQ CGP40215A; BIS[[3-(AMINOIMINOMETHYL)PHENYL]METHYLENE] HETSYN 2 CGQ CARBONIMIDIC DIHYDRAZIDE FORMUL 3 MG MG 2+ FORMUL 4 CGQ C17 H22 N9 3+ FORMUL 5 HOH *117(H2 O) LINK MG MG A4026 O HOH A8113 1555 1555 2.01 LINK MG MG A4026 O HOH A8114 1555 1555 2.03 LINK MG MG A4026 O HOH A8115 1555 1555 2.02 LINK MG MG A4026 O HOH A8116 1555 1555 2.02 LINK MG MG A4026 O HOH A8117 1555 1555 2.02 LINK MG MG A4026 O HOH B8112 1555 1555 2.02 SITE 1 AC1 14 DG A1004 DA A1006 DT A1007 DT A1008 SITE 2 AC1 14 DC A1009 DA B2018 DT B2019 DT B2020 SITE 3 AC1 14 DC B2021 HOH B8017 HOH B8030 HOH B8033 SITE 4 AC1 14 HOH B8045 HOH B8099 SITE 1 AC2 6 HOH A8113 HOH A8114 HOH A8115 HOH A8116 SITE 2 AC2 6 HOH A8117 HOH B8112 CRYST1 24.098 39.821 65.620 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 0.041497 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025112 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015239 0.00000