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- PDB-4u8b: Crystal structure of D(CGCGAATTCGCG)2 complexed with BPH-1358 -

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Basic information

Entry
Database: PDB / ID: 4u8b
TitleCrystal structure of D(CGCGAATTCGCG)2 complexed with BPH-1358
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA/ANTIBIOTIC / Antibacterial Agents / Bisamidines / Minor Groove Binders / Models / Molecular / Nucleic Acid Conformation / Oligodeoxyribonucleotides / DNA-ANTIBIOTIC complex
Function / homologyChem-3F2 / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsZhu, W. / Oldfield, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM065307 United States
CitationJournal: J.Med.Chem. / Year: 2015
Title: Antibacterial drug leads: DNA and enzyme multitargeting.
Authors: Zhu, W. / Wang, Y. / Li, K. / Gao, J. / Huang, C.H. / Chen, C.C. / Ko, T.P. / Zhang, Y. / Guo, R.T. / Oldfield, E.
History
DepositionAug 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,8804
Polymers7,3272
Non-polymers5532
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-5 kcal/mol
Surface area4340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.765, 39.388, 65.362
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (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 / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-3F2 / N,N'-bis[3-(4,5-dihydro-1H-imidazol-2-yl)phenyl]biphenyl-4,4'-dicarboxamide / BPH-1358


Mass: 528.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H28N6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.9
Details: 40 mM sodium cacodylate, pH 6.9, 50 mM Mg(OAc)2, 6 mM spermine-4HCl, 40% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.31→50 Å / Num. obs: 15205 / % possible obs: 98.7 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.076 / Χ2: 1.063 / Net I/av σ(I): 29.844 / Net I/σ(I): 10.8 / Num. measured all: 203452
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.31-1.3314.30.6597310.749100
1.33-1.3614.40.547640.756100
1.36-1.3814.40.4647470.762100
1.38-1.4114.30.3847600.786100
1.41-1.4414.40.3197350.831100
1.44-1.4814.50.2697740.857100
1.48-1.5114.40.2167420.873100
1.51-1.5514.40.1877600.934100
1.55-1.614.20.1537641.08100
1.6-1.65140.1197611.158100
1.65-1.7113.90.1057751.234100
1.71-1.7813.80.0937451.236100
1.78-1.8613.80.0837761.19100
1.86-1.9613.70.0777671.265100
1.96-2.0813.50.0747651.332100
2.08-2.2412.90.0747791.41100
2.24-2.4712.60.0717851.367100
2.47-2.8212.10.067921.212100
2.82-3.5610.60.0617471.18493.1
3.56-507.30.0647361.32183.7

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Processing

Software
NameVersionClassification
HKL-3000data reduction
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPCCP4 6.2.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 436D

436d


Resolution: 1.31→16.87 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.077 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.246 759 5 %RANDOM
Rwork0.2415 14400 --
obs0.2417 15159 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.98 Å2 / Biso mean: 21.421 Å2 / Biso min: 11.55 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.31→16.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 41 43 570
Biso mean--38.89 23.89 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.012589
X-RAY DIFFRACTIONr_angle_refined_deg2.7551.469898
X-RAY DIFFRACTIONr_chiral_restr0.1140.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0360.021304
LS refinement shellResolution: 1.31→1.344 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 37 -
Rwork0.271 918 -
all-955 -
obs--97.05 %

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