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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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