HEADER DNA 20-SEP-05 2B3E TITLE CRYSTAL STRUCTURE OF DB819-D(CGCGAATTCGCG)2 COMPLEX. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 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; SOURCE 3 OTHER_DETAILS: AT-RICH REGION IN THE GENOME OF ORGANISMS. KEYWDS NUCLEIC ACIDS, DNA, DOUBLE HELIX, MINOR GROOVE, DNA MINOR, GROOVE KEYWDS 2 BINDER, DNA MINOR GROOVE-LIGAND COMPLEX, DB819, A2T2, DICKERSON AND KEYWDS 3 DREW DODECAMER, CRYSTAL STRUCTURE OF B-DNA, DNA-DRUG COMPLEX, KEYWDS 4 MAGNESIUM-WATER COMPLEX, HYDRATED MAGNESIUM, DNA HYDRATION. EXPDTA X-RAY DIFFRACTION AUTHOR N.H.CAMPBELL,D.A.EVANS,M.P.LEE,G.N.PARKINSON,S.NEIDLE REVDAT 6 23-AUG-23 2B3E 1 REMARK LINK REVDAT 5 24-JUL-19 2B3E 1 REMARK REVDAT 4 24-FEB-09 2B3E 1 VERSN REVDAT 3 13-DEC-05 2B3E 1 AUTHOR REVDAT 2 06-DEC-05 2B3E 1 JRNL REVDAT 1 22-NOV-05 2B3E 0 JRNL AUTH N.H.CAMPBELL,D.A.EVANS,M.P.LEE,G.N.PARKINSON,S.NEIDLE JRNL TITL TARGETING THE DNA MINOR GROOVE WITH FUSED RING DICATIONIC JRNL TITL 2 COMPOUNDS: COMPARISON OF IN SILICO SCREENING AND A JRNL TITL 3 HIGH-RESOLUTION CRYSTAL STRUCTURE. JRNL REF BIOORG.MED.CHEM.LETT. V. 16 15 2006 JRNL REFN ISSN 0960-894X JRNL PMID 16263285 JRNL DOI 10.1016/J.BMCL.2005.10.036 REMARK 2 REMARK 2 RESOLUTION. 1.36 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) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.0 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) : 0.210 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.208 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.005 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1308 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 13073 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.199 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.196 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.048 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1147 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 11415 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 : 31 REMARK 3 SOLVENT ATOMS : 107 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 624.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2511 REMARK 3 NUMBER OF RESTRAINTS : 2558 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 0.032 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.036 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.009 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.009 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.046 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 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 : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED WEIGHTED FULL MATRIX LEAST SQUARES REMARK 3 PROCEDURE. ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, REMARK 3 MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 REMARK 4 REMARK 4 2B3E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000034625. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 105.0 REMARK 200 PH : 7.00 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) : 1.54178 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : OSMIC FOCUSING MIRROR SYSTEM REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13180 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 4.380 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 56.8200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.030 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: DNA PART OF NDB ENTRY GDL009 OR PDB ENTRY 2DBE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM CHLORIDE, DNA, COMPOUND REMARK 280 DB819, MPD, SODIUM CACODYLATE BUFFER, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K, PH 7.00 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 12.09800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.76250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.98000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.76250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.09800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.98000 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N26 DBN A 25 O HOH A 43 2.10 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. = -4.3 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DG A 2 C5 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = -5.5 DEGREES REMARK 500 DA A 6 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DG A 10 N1 - C6 - O6 ANGL. DEV. = 6.5 DEGREES REMARK 500 DG A 10 C5 - C6 - O6 ANGL. DEV. = -5.0 DEGREES REMARK 500 DC A 11 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = -6.5 DEGREES REMARK 500 DG A 12 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 DC B 13 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = -7.2 DEGREES REMARK 500 DC B 15 C2 - N3 - C4 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC B 15 C5 - C4 - N4 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA B 17 C6 - N1 - C2 ANGL. DEV. = 4.6 DEGREES REMARK 500 DA B 17 N1 - C2 - N3 ANGL. DEV. = -5.0 DEGREES REMARK 500 DA B 18 C6 - N1 - C2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT B 20 O4' - C1' - N1 ANGL. DEV. = -6.9 DEGREES REMARK 500 DC B 21 O4' - C1' - N1 ANGL. DEV. = -8.8 DEGREES REMARK 500 DG B 22 C3' - C2' - C1' ANGL. DEV. = -6.3 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 A 26 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 129 O REMARK 620 2 HOH A 130 O 88.6 REMARK 620 3 HOH A 132 O 89.9 89.0 REMARK 620 4 HOH A 133 O 90.3 91.9 179.0 REMARK 620 5 HOH B 128 O 91.8 179.6 90.9 88.1 REMARK 620 6 HOH B 131 O 179.2 90.6 90.1 89.7 89.0 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 DBN A 25 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: GDL009 RELATED DB: NDB REMARK 900 DNA COMPONENT. REMARK 900 RELATED ID: 2DBE RELATED DB: PDB REMARK 900 DNA COMPONENT. REMARK 900 RELATED ID: DD0069 RELATED DB: NDB REMARK 900 RELATED ID: 1VZK RELATED DB: PDB REMARK 900 RELATED ID: 2B0K RELATED DB: PDB REMARK 900 RELATED ID: 2B2B RELATED DB: PDB DBREF 2B3E A 1 12 PDB 2B3E 2B3E 1 12 DBREF 2B3E B 13 24 PDB 2B3E 2B3E 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 DBN A 25 30 HETNAM MG MAGNESIUM ION HETNAM DBN 6-(4,5-DIHYDRO-1H-IMIDAZOL-2-YL)-2-{5-[4-(4,5-DIHYDRO- HETNAM 2 DBN 1H-IMIDAZOL-2-YL)PHENYL]THIEN-2-YL}-1H-BENZIMIDAZOLE HETSYN DBN DB819 FORMUL 3 MG MG 2+ FORMUL 4 DBN C23 H20 N6 S FORMUL 5 HOH *107(H2 O) LINK MG MG A 26 O HOH A 129 1555 1555 2.13 LINK MG MG A 26 O HOH A 130 1555 1555 2.11 LINK MG MG A 26 O HOH A 132 1555 1555 2.12 LINK MG MG A 26 O HOH A 133 1555 1555 2.13 LINK MG MG A 26 O HOH B 128 1555 1555 2.11 LINK MG MG A 26 O HOH B 131 1555 1555 2.11 SITE 1 AC1 6 HOH A 129 HOH A 130 HOH A 132 HOH A 133 SITE 2 AC1 6 HOH B 128 HOH B 131 SITE 1 AC2 12 DA A 6 DT A 7 DT A 8 DC A 9 SITE 2 AC2 12 HOH A 43 HOH A 80 HOH A 95 DA B 18 SITE 3 AC2 12 DT B 19 DT B 20 DC B 21 HOH B 79 CRYST1 24.196 39.960 65.525 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 0.041329 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025025 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015261 0.00000