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- PDB-7v9h: The BEN3 domain of protein Bend3 -

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Basic information

Entry
Database: PDB / ID: 7v9h
TitleThe BEN3 domain of protein Bend3
ComponentsBEN domain-containing protein 3
KeywordsDNA BINDING PROTEIN
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
BEN domain-containing protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.692 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


Theoretical massNumber of molelcules
Total (without water)12,6421
Polymers12,6421
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6590 Å2
Unit cell
Length a, b, c (Å)54.011, 54.011, 70.772
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein BEN domain-containing protein 3


Mass: 12642.411 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 1.0 M DL-Malic acid, pH 7.0 and 0.1 M BIS-TRIS propane, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97885 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 3542 / % possible obs: 99.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 87.9
Reflection shellResolution: 2.69→2.8 Å / Rmerge(I) obs: 0.159 / Num. unique obs: 335

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.692→46.775 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 13.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2189 181 5.12 %
Rwork0.1796 3351 -
obs0.1815 3532 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.59 Å2 / Biso mean: 20.5938 Å2 / Biso min: 6.94 Å2
Refinement stepCycle: final / Resolution: 2.692→46.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms824 0 0 36 860
Biso mean---24.96 -
Num. residues----102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004849
X-RAY DIFFRACTIONf_angle_d0.6491143
X-RAY DIFFRACTIONf_chiral_restr0.039124
X-RAY DIFFRACTIONf_plane_restr0.004148
X-RAY DIFFRACTIONf_dihedral_angle_d15.812521
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2189 181 -
Rwork0.1796 3351 -
obs--99 %

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