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- PDB-2b0k: Crystal structure of the DB921-D(CGCGAATTCGCG)2 complex. -

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Basic information

Entry
Database: PDB / ID: 2b0k
TitleCrystal structure of the DB921-D(CGCGAATTCGCG)2 complex.
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
KeywordsDNA / NUCLEIC ACIDS / DOUBLE HELIX / MINOR GROOVE / DNA MINOR GROOVE BINDER / DNA MINOR GROOVE-LIGAND COMPLEX / DB921 / A2T2 / DICKERSON AND DREW DNA / CRYSTAL STRUCTURE OF B-DNA / DNA-DRUG COMPLEX / MAGNESIUM-WATER COMPLEX / HYDRATED MAGNESIUM / DNA HYDRATION.
Function / homologyChem-D2A / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMiao, Y. / Lee, M.P. / Parkinson, G.N. / Batista-Parra, A. / Ismail, M.A. / Neidle, S. / Boykin, D.W. / Wilson, W.D.
CitationJournal: Biochemistry / Year: 2005
Title: Out-of-Shape DNA Minor Groove Binders: Induced Fit Interactions of Heterocyclic Dications with the DNA Minor Groove.
Authors: Miao, Y. / Lee, M.P. / Parkinson, G.N. / Batista-Parra, A. / Ismail, M.A. / Neidle, S. / Boykin, D.W. / Wilson, W.D.
History
DepositionSep 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7054
Polymers7,3272
Non-polymers3792
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.288, 40.068, 65.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: AT-RICH REGION IN THE GENOME OF ORGANISMS.
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-D2A / 2-(4'-AMIDINOBIPHENYL-4-YL)-1H-BENZIMIDAZOLE-5-AMIDINE / DB921


Mass: 354.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18N6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 293 K / pH: 6.5
Details: MAGNESIUM CHLORIDE, DNA, COMPOUND DB921, MPD, SODIUM CACODYLATE BUFFER, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K, pH 6.50
Components of the solutions
IDNameCrystal-IDSol-ID
1MAGNESIUM CHLORIDE11
2DB92111
3MPD11
4SODIUM CACODYLATE11
5H2O11
6MAGNESIUM CHLORIDE12
7DB92112
8SODIUM CACODYLATE12
9H2O12

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 2005 / Details: OSMIC FOCUSING MIRROR SYSTEM
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.64→25 Å / Num. obs: 8055 / % possible obs: 96.6 % / Observed criterion σ(I): -2 / Redundancy: 3.16 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 36.19
Reflection shellResolution: 1.64→1.7 Å / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 6.43 / % possible all: 96.4

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DNA PART OF NDB ENTRY GDL009 OR PDB ENTRY 2DBE

2dbe


Resolution: 1.64→8 Å / Num. parameters: 2399 / Num. restraintsaints: 2543 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE. ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.3002 784 9.84 %RANDOM
all0.2307 7968 --
obs0.2286 -87.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 596
Refinement stepCycle: LAST / Resolution: 1.64→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 34 76 596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.009
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.037
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.026
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.067
X-RAY DIFFRACTIONs_approx_iso_adps0

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