HEADER DNA 14-SEP-05 2B0K TITLE CRYSTAL STRUCTURE OF THE DB921-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, DB921, A2T2, DICKERSON AND KEYWDS 3 DREW DNA, CRYSTAL STRUCTURE OF B-DNA, DNA-DRUG COMPLEX, MAGNESIUM- KEYWDS 4 WATER COMPLEX, HYDRATED MAGNESIUM, DNA HYDRATION. EXPDTA X-RAY DIFFRACTION AUTHOR Y.MIAO,M.P.LEE,G.N.PARKINSON,A.BATISTA-PARRA,M.A.ISMAIL,S.NEIDLE, AUTHOR 2 D.W.BOYKIN,W.D.WILSON REVDAT 5 23-AUG-23 2B0K 1 REMARK LINK REVDAT 4 24-JUL-19 2B0K 1 REMARK REVDAT 3 24-FEB-09 2B0K 1 VERSN REVDAT 2 13-DEC-05 2B0K 1 AUTHOR REVDAT 1 22-NOV-05 2B0K 0 JRNL AUTH Y.MIAO,M.P.LEE,G.N.PARKINSON,A.BATISTA-PARRA,M.A.ISMAIL, JRNL AUTH 2 S.NEIDLE,D.W.BOYKIN,W.D.WILSON JRNL TITL OUT-OF-SHAPE DNA MINOR GROOVE BINDERS: INDUCED FIT JRNL TITL 2 INTERACTIONS OF HETEROCYCLIC DICATIONS WITH THE DNA MINOR JRNL TITL 3 GROOVE. JRNL REF BIOCHEMISTRY V. 44 14701 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 16274217 JRNL DOI 10.1021/BI051791Q REMARK 2 REMARK 2 RESOLUTION. 1.64 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.2 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) : 0.231 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.229 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.300 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 9.840 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 784 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 7968 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.217 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.214 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 9.840 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 683 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 6942 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 : 28 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 596.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2399 REMARK 3 NUMBER OF RESTRAINTS : 2543 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 ANGLE DISTANCES (A) : 0.019 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.009 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.037 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.026 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.067 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 2B0K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034524. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 105.0 REMARK 200 PH : 6.50 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 : 8055 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 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 (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.160 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 36.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.19700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.430 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 (%): 54.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM CHLORIDE, DNA, COMPOUND REMARK 280 DB921, MPD, SODIUM CACODYLATE BUFFER, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293.0K, PH 6.50 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 12.14400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.99450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.03400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.99450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.14400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.03400 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 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 104 O REMARK 620 2 HOH A 105 O 90.0 REMARK 620 3 HOH A 108 O 90.0 90.0 REMARK 620 4 HOH B 103 O 90.0 180.0 90.0 REMARK 620 5 HOH B 106 O 179.9 90.0 89.9 90.0 REMARK 620 6 HOH B 107 O 90.0 90.0 179.9 90.0 90.0 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 D2A A 25 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: GDL009 RELATED DB: NDB REMARK 900 DNA PART OF NDB ENTRY GDL009 REMARK 900 RELATED ID: 2DBE RELATED DB: PDB REMARK 900 DNA PART OF PDB ENTRY 2DBE DBREF 2B0K A 1 12 PDB 2B0K 2B0K 1 12 DBREF 2B0K B 13 24 PDB 2B0K 2B0K 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 D2A A 25 27 HETNAM MG MAGNESIUM ION HETNAM D2A 2-(4'-AMIDINOBIPHENYL-4-YL)-1H-BENZIMIDAZOLE-5-AMIDINE HETSYN D2A DB921 FORMUL 3 MG MG 2+ FORMUL 4 D2A C21 H18 N6 FORMUL 5 HOH *82(H2 O) LINK MG MG A 26 O HOH A 104 1555 1555 2.13 LINK MG MG A 26 O HOH A 105 1555 1555 2.13 LINK MG MG A 26 O HOH A 108 1555 1555 2.13 LINK MG MG A 26 O HOH B 103 1555 1555 2.12 LINK MG MG A 26 O HOH B 106 1555 1555 2.13 LINK MG MG A 26 O HOH B 107 1555 1555 2.13 SITE 1 AC1 6 HOH A 104 HOH A 105 HOH A 108 HOH B 103 SITE 2 AC1 6 HOH B 106 HOH B 107 SITE 1 AC2 8 DA A 6 DT A 7 DT A 8 DC A 9 SITE 2 AC2 8 DA B 18 DT B 19 DT B 20 DC B 21 CRYST1 24.288 40.068 65.989 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 0.041173 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024958 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015154 0.00000