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- PDB-7yuk: Complex structure of BANP BEN domain bound to DNA -

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Basic information

Entry
Database: PDB / ID: 7yuk
TitleComplex structure of BANP BEN domain bound to DNA
Components
  • DNA (5'-D(*CP*TP*CP*TP*CP*GP*CP*GP*AP*GP*AP*G)-3')
  • Protein BANP
KeywordsDNA BINDING PROTEIN / BANP-DNA complex structure
Function / homology
Function and homology information


Regulation of TP53 Activity through Association with Co-factors / protein localization to nucleus / negative regulation of protein catabolic process / chromatin organization / nuclear body / cell cycle / DNA binding / nucleoplasm / identical protein binding
Similarity search - Function
Protein BANP / BEN domain / BEN domain / BEN domain profile. / BEN
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein BANP
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsZhang, J. / Xiao, Y.Q. / Chen, Y.X. / Liu, K. / Min, J.R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770834 China
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural insights into DNA recognition by the BEN domain of the transcription factor BANP.
Authors: Liu, K. / Zhang, J. / Xiao, Y. / Yang, A. / Song, X. / Li, Y. / Chen, Y. / Hughes, T.R. / Min, J.
History
DepositionAug 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 31, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,6644
Polymers23,5723
Non-polymers921
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-19 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.965, 129.900, 40.133
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Protein BANP / BEN domain-containing protein 1 / Btg3-associated nuclear protein / Scaffold/matrix-associated ...BEN domain-containing protein 1 / Btg3-associated nuclear protein / Scaffold/matrix-associated region-1-binding protein


Mass: 16245.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BANP, BEND1, SMAR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N9N5
#2: DNA chain DNA (5'-D(*CP*TP*CP*TP*CP*GP*CP*GP*AP*GP*AP*G)-3')


Mass: 3663.392 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.04 Å3/Da / Density % sol: 39.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% w/v PEG3350; 0.02 M Sodium/potassium phosphate; 0.1 M Bris-Tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 11802 / % possible obs: 99.9 % / Redundancy: 12.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Net I/σ(I): 17
Reflection shellResolution: 2.11→2.17 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 927 / CC1/2: 0.978 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YUG

7yug


Resolution: 2.11→40.17 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.797 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 615 5.2 %RANDOM
Rwork0.2246 ---
obs0.2266 11149 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.92 Å2 / Biso mean: 40.692 Å2 / Biso min: 21.67 Å2
Baniso -1Baniso -2Baniso -3
1-5.88 Å20 Å20 Å2
2---2.73 Å20 Å2
3----3.15 Å2
Refinement stepCycle: final / Resolution: 2.11→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 486 6 55 1496
Biso mean--62.25 39.46 -
Num. residues----140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121519
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181168
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.4612147
X-RAY DIFFRACTIONr_angle_other_deg1.4141.9182719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5375115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.42320.51758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.54115179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2661510
X-RAY DIFFRACTIONr_chiral_restr0.0750.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021368
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02350
LS refinement shellResolution: 2.11→2.162 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.317 38 -
Rwork0.317 796 -
obs--99.4 %

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