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- PDB-4u8c: Crystal structure of D(CGCGAATTCGCG)2 complexed with BPH-1409 -

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Basic information

Entry
Database: PDB / ID: 4u8c
TitleCrystal structure of D(CGCGAATTCGCG)2 complexed with BPH-1409
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-3F6 / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 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 / Other / Source and taxonomy / Structure summary
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
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 / refine_hist / 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 / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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)7,8244
Polymers7,3272
Non-polymers4972
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-5 kcal/mol
Surface area4390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.793, 39.948, 65.786
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-3F6 / 2,2'-benzene-1,4-diylbis[6-(1,4,5,6-tetrahydropyrimidin-2-yl)-1H-indole]


Mass: 472.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H28N6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
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 17, 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: 1.24→50 Å / Num. obs: 18244 / % possible obs: 95 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.068 / Χ2: 1.023 / Net I/av σ(I): 35.586 / Net I/σ(I): 11.9 / Num. measured all: 251444
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.24-1.2612.10.5517600.70883.2
1.26-1.2812.50.4928030.70285.5
1.28-1.3112.70.4328380.70588
1.31-1.3413.20.4138720.71593.9
1.34-1.3613.20.3269250.73797.5
1.36-1.413.80.3179260.73199.1
1.4-1.4314.50.2449590.762100
1.43-1.4714.40.2079550.748100
1.47-1.5114.60.1629250.812100
1.51-1.5614.50.1359600.906100
1.56-1.6214.50.1089461.093100
1.62-1.6814.50.0939541.167100
1.68-1.7614.50.089751.128100
1.76-1.8514.50.0729301.101100
1.85-1.9714.40.0659791.08999.9
1.97-2.1214.40.0679671.2999.8
2.12-2.3314.20.0719671.595100
2.33-2.6714.10.0599901.401100
2.67-3.3713.30.0569271.47192.4
3.37-5010.10.0566861.49463.4

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Processing

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

436d


Resolution: 1.24→17.07 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.894 / SU B: 1.573 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3329 940 5.2 %RANDOM
Rwork0.2761 17254 --
obs0.2789 18194 94.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 43.77 Å2 / Biso mean: 23.728 Å2 / Biso min: 14.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.24→17.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 37 47 570
Biso mean--30.78 28.12 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.011586
X-RAY DIFFRACTIONr_angle_refined_deg2.3281.464896
X-RAY DIFFRACTIONr_chiral_restr0.10.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0290.02292
LS refinement shellResolution: 1.24→1.272 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 48 -
Rwork0.425 976 -
all-1024 -
obs--81.33 %

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