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- PDB-7yun: Crystal structure of human BEND6 BEN domain in complex with methy... -

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Basic information

Entry
Database: PDB / ID: 7yun
TitleCrystal structure of human BEND6 BEN domain in complex with methylated DNA
Components
  • BEN domain-containing protein 6
  • DNA (5'-D(*CP*TP*CP*TP*CP*GP*(5CM)P*GP*AP*GP*AP*G)-3')
KeywordsDNA BINDING PROTEIN / BEND6-DNA complex
Function / homology
Function and homology information


negative regulation of Notch signaling pathway / positive regulation of neuron differentiation / transcription corepressor activity / nervous system development / chromatin binding / DNA binding / nucleus
Similarity search - Function
BEN domain-containing protein 6 / BEN domain / BEN domain / BEN domain / BEN domain profile. / BEN / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / BEN domain-containing protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsLiu, K. / Xiao, Y.Q. / Zhang, J. / 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 1.0May 3, 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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BEN domain-containing protein 6
B: BEN domain-containing protein 6
C: DNA (5'-D(*CP*TP*CP*TP*CP*GP*(5CM)P*GP*AP*GP*AP*G)-3')
D: DNA (5'-D(*CP*TP*CP*TP*CP*GP*(5CM)P*GP*AP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)30,9684
Polymers30,9684
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-8 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.482, 67.276, 53.019
Angle α, β, γ (deg.)90.00, 100.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BEN domain-containing protein 6 / BEND6


Mass: 11806.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BEND6, C6orf65 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SZJ8
#2: DNA chain DNA (5'-D(*CP*TP*CP*TP*CP*GP*(5CM)P*GP*AP*GP*AP*G)-3')


Mass: 3677.419 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M carboxylic acids, 0.1 M imidazole, 0.1 M MES monohydrate (acid) (pH 6.5), 12.5% MPD (v/v), 12.5 % PEG 1000 (v/v), and 12.5% PEG 3350 (w/v).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: May 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.13→34.34 Å / Num. obs: 15367 / % possible obs: 99.9 % / Redundancy: 4.77 % / Rmerge(I) obs: 0.0559 / Net I/σ(I): 17.36
Reflection shellResolution: 2.13→2.16 Å / Redundancy: 3.14 % / Rmerge(I) obs: 0.2398 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 622 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SAINT5.8.0267data scaling
SAINT3.27data reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YUK

7yuk


Resolution: 2.13→34.34 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.741 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23356 780 5.1 %RANDOM
Rwork0.18447 ---
obs0.18694 14571 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.344 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.13→34.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 488 0 155 2108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122031
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181735
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.5452835
X-RAY DIFFRACTIONr_angle_other_deg1.3861.824011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.665181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.46124.10378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60315298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.259158
X-RAY DIFFRACTIONr_chiral_restr0.080.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021969
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8542.371730
X-RAY DIFFRACTIONr_mcbond_other1.8512.369729
X-RAY DIFFRACTIONr_mcangle_it2.7993.544909
X-RAY DIFFRACTIONr_mcangle_other2.7983.546910
X-RAY DIFFRACTIONr_scbond_it2.4372.5851301
X-RAY DIFFRACTIONr_scbond_other2.4372.5851300
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7793.8041927
X-RAY DIFFRACTIONr_long_range_B_refined5.42926.3772530
X-RAY DIFFRACTIONr_long_range_B_other5.33726.1992502
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 63 -
Rwork0.189 1071 -
obs--99.91 %

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