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- PDB-8htx: Crystal structure of BANP in complex with methylated DNA -

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Basic information

Entry
Database: PDB / ID: 8htx
TitleCrystal structure of BANP in complex with methylated DNA
Components
  • DNA (5'-D(*CP*TP*CP*TP*(5CM)P*GP*CP*GP*AP*GP*AP*G)-3')
  • Protein BANP
KeywordsDNA BINDING PROTEIN / BANP / BEN Domain
Function / homology
Function and homology information


Regulation of TP53 Activity through Association with Co-factors / chromatin organization / nuclear speck / nuclear body / DNA binding / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
Protein BANP / 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) / Protein BANP
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhang, J. / Min, J. / Liu, K.
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
DepositionDec 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.type

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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*(5CM)P*GP*CP*GP*AP*GP*AP*G)-3')
D: DNA (5'-D(*CP*TP*CP*TP*(5CM)P*GP*CP*GP*AP*GP*AP*G)-3')
B: Protein BANP
E: DNA (5'-D(*CP*TP*CP*TP*(5CM)P*GP*CP*GP*AP*GP*AP*G)-3')
F: DNA (5'-D(*CP*TP*CP*TP*(5CM)P*GP*CP*GP*AP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)47,2006
Polymers47,2006
Non-polymers00
Water00
1
A: Protein BANP
C: DNA (5'-D(*CP*TP*CP*TP*(5CM)P*GP*CP*GP*AP*GP*AP*G)-3')
D: DNA (5'-D(*CP*TP*CP*TP*(5CM)P*GP*CP*GP*AP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)23,6003
Polymers23,6003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-6 kcal/mol
Surface area10050 Å2
MethodPISA
2
B: Protein BANP
E: DNA (5'-D(*CP*TP*CP*TP*(5CM)P*GP*CP*GP*AP*GP*AP*G)-3')
F: DNA (5'-D(*CP*TP*CP*TP*(5CM)P*GP*CP*GP*AP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)23,6003
Polymers23,6003
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-9 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.352, 92.645, 127.022
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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.: 2
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*(5CM)P*GP*CP*GP*AP*GP*AP*G)-3')


Mass: 3677.419 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium fluoride, 0.1 M BTP-tris (pH 6.5), 20 % PEG3350 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→38.51 Å / Num. obs: 12915 / % possible obs: 99.7 % / Redundancy: 10.8 % / CC1/2: 0.995 / Net I/σ(I): 12.6
Reflection shellResolution: 2.8→2.95 Å / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1818 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
autoPROCdata processing
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The solved BANP structure in this study

Resolution: 2.8→31.76 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2723 646 5.09 %
Rwork0.2322 --
obs0.2344 12691 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→31.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 976 0 0 2882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043040
X-RAY DIFFRACTIONf_angle_d0.6364303
X-RAY DIFFRACTIONf_dihedral_angle_d25.779709
X-RAY DIFFRACTIONf_chiral_restr0.037459
X-RAY DIFFRACTIONf_plane_restr0.005384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.020.48661290.3682381X-RAY DIFFRACTION99
3.02-3.320.39291250.33332291X-RAY DIFFRACTION96
3.32-3.80.32921200.24662372X-RAY DIFFRACTION97
3.8-4.780.26421250.20742447X-RAY DIFFRACTION100
4.78-31.760.2021470.19482554X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 10.9571 Å / Origin y: 24.8565 Å / Origin z: 12.579 Å
111213212223313233
T0.5324 Å2-0.0119 Å20.1045 Å2-0.6068 Å20.0119 Å2--0.5201 Å2
L0.3738 °2-0.1138 °21.4573 °2-0.5424 °2-0.0584 °2--2.1091 °2
S0.0017 Å °0.0394 Å °-0.0811 Å °-0.0304 Å °0.0672 Å °-0.0551 Å °0.2947 Å °0.0489 Å °-0.0221 Å °
Refinement TLS groupSelection details: all

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