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- PDB-7v9i: The Monomer mutant of BEN4 domain of protein Bend3 with DNA -

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Basic information

Entry
Database: PDB / ID: 7v9i
TitleThe Monomer mutant of BEN4 domain of protein Bend3 with DNA
Components
  • BEN domain-containing protein 3
  • DNA (5'-D(*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*C)-3')
  • DNA (5'-D(*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*T)-3')
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of ATP metabolic process / rDNA binding / rDNA heterochromatin formation / negative regulation of transcription by RNA polymerase I / heterochromatin / protein homooligomerization / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
BEN domain-containing protein 3 / BEN domain / BEN domain / BEN domain profile. / BEN
Similarity search - Domain/homology
DNA / DNA (> 10) / BEN domain-containing protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 3.5 Å
AuthorsZhang, J. / Zhang, Y. / You, Q. / Huang, C. / Zhang, T. / Wang, M. / Zhang, T. / Yang, X. / Xiong, J. / Li, Y. ...Zhang, J. / Zhang, Y. / You, Q. / Huang, C. / Zhang, T. / Wang, M. / Zhang, T. / Yang, X. / Xiong, J. / Li, Y. / Liu, C.P. / Zhang, Z. / Xu, R.M. / Zhu, B.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0508900, 2017YFA0504202 China
National Science Foundation (NSF, China)31991162, 31521002 China
Chinese Academy of SciencesXDB 37010100 China
CitationJournal: Science / Year: 2022
Title: Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation.
Authors: Zhang, J. / Zhang, Y. / You, Q. / Huang, C. / Zhang, T. / Wang, M. / Zhang, T. / Yang, X. / Xiong, J. / Li, Y. / Liu, C.P. / Zhang, Z. / Xu, R.M. / Zhu, B.
History
DepositionAug 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BEN domain-containing protein 3
B: DNA (5'-D(*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*T)-3')
C: DNA (5'-D(*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)20,8633
Polymers20,8633
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-24 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.504, 61.990, 136.024
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein BEN domain-containing protein 3


Mass: 13533.777 Da / Num. of mol.: 1 / Mutation: V78R, E788A, M791N, E792D, E793R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bend3 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6PAL0
#2: DNA chain DNA (5'-D(*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*T)-3')


Mass: 3624.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*C)-3')


Mass: 3704.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium formate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 2848 / % possible obs: 95.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.209 / Net I/σ(I): 6.1
Reflection shellResolution: 3.5→3.63 Å / Rmerge(I) obs: 0.461 / Num. unique obs: 292

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.5→34.01 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 158 5.69 %
Rwork0.2107 2617 -
obs0.2139 2775 94.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.38 Å2 / Biso mean: 43.6291 Å2 / Biso min: 24.12 Å2
Refinement stepCycle: final / Resolution: 3.5→34.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms877 486 0 0 1363
Num. residues----129
LS refinement shellResolution: 3.5→3.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2608 158 -
Rwork0.2107 2617 -
all-2775 -
obs--94 %

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