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- PDB-5ybx: Crystal structure of the N-terminal domain of Bqt4 in S.pombe -

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Basic information

Entry
Database: PDB / ID: 5ybx
TitleCrystal structure of the N-terminal domain of Bqt4 in S.pombe
ComponentsBouquet formation protein 4
KeywordsDNA BINDING PROTEIN / Telomere bouquet / Nuclear envelope / Chromosome organization
Function / homology
Function and homology information


meiotic telomere tethering at nuclear periphery / telomere-nuclear envelope anchor activity / nuclear membrane complex Bqt3-Bqt4 / mitotic telomere tethering at nuclear periphery / meiotic attachment of telomere to nuclear envelope / meiotic telomere clustering / nuclear inner membrane / telomere organization / telomere maintenance / nuclear envelope ...meiotic telomere tethering at nuclear periphery / telomere-nuclear envelope anchor activity / nuclear membrane complex Bqt3-Bqt4 / mitotic telomere tethering at nuclear periphery / meiotic attachment of telomere to nuclear envelope / meiotic telomere clustering / nuclear inner membrane / telomere organization / telomere maintenance / nuclear envelope / cell division / DNA binding / nucleus / cytoplasm
Similarity search - Function
Bouquet formation protein 4 / Transcription regulator HTH, APSES-type DNA-binding domain / KilA, N-terminal/APSES-type HTH, DNA-binding / HTH APSES-type DNA-binding domain superfamily / APSES-type HTH DNA-binding domain profile. / KilA-N
Similarity search - Domain/homology
Bouquet formation protein 4
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.501 Å
AuthorsHu, C. / Chen, Y.
CitationJournal: Structure / Year: 2019
Title: The Inner Nuclear Membrane Protein Bqt4 in Fission Yeast Contains a DNA-Binding Domain Essential for Telomere Association with the Nuclear Envelope.
Authors: Hu, C. / Inoue, H. / Sun, W. / Takeshita, Y. / Huang, Y. / Xu, Y. / Kanoh, J. / Chen, Y.
History
DepositionSep 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bouquet formation protein 4


Theoretical massNumber of molelcules
Total (without water)16,1931
Polymers16,1931
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The protein exists as a monomer judged by gel-filtration.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7290 Å2
Unit cell
Length a, b, c (Å)94.658, 94.658, 94.658
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Bouquet formation protein 4


Mass: 16192.589 Da / Num. of mol.: 1 / Fragment: UNP residues 2-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: bqt4, SPBC19C7.10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O60158

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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: 2.37 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 30% PEG4000, 0.2 M Ammonium acetate, 0.1 M Sodium citrate, pH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97845 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 2.5→33.467 Å / Num. obs: 9479 / % possible obs: 99.9 % / Redundancy: 1 % / Biso Wilson estimate: 75.34 Å2 / Net I/σ(I): 1.9
Reflection shell

Diffraction-ID: 1 / Redundancy: 10 % / % possible all: 100

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.5-2.540.6992470.9160.1580.7170.534
2.54-2.590.5892330.9310.1350.6040.553
2.59-2.640.5212450.9190.1190.5350.578
2.64-2.690.4872590.9260.1120.50.625
2.69-2.750.4132520.9590.0970.4240.659
2.75-2.820.3232310.9750.0780.3330.818
2.82-2.890.2792580.980.0650.2870.876
2.89-2.960.2372500.9830.0530.2431.039
2.96-3.050.2012480.9880.0460.2061.108
3.05-3.150.1792490.9910.0410.1841.315
3.15-3.260.162480.9910.0370.1641.485
3.26-3.390.1332440.9950.0320.1371.919
3.39-3.550.1222540.9960.030.1262.136
3.55-3.730.1042570.9960.0260.1082.037
3.73-3.970.0972470.9980.0230.12.272
3.97-4.270.0882490.9970.0210.093.425
4.27-4.70.0762560.9940.0180.0792.722
4.7-5.380.082580.9970.020.0822.991
5.38-6.780.0782610.9970.0180.083.209
6.78-70.0852790.9970.0220.0886.765

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
HKL-2000data scaling
SHARPphasing
PDB_EXTRACT3.22data extraction
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.501→33.467 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 33.35
RfactorNum. reflection% reflection
Rfree0.2669 960 10.13 %
Rwork0.2236 --
obs0.228 9479 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.82 Å2 / Biso mean: 70 Å2 / Biso min: 40.23 Å2
Refinement stepCycle: final / Resolution: 2.501→33.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 0 0 0 1021
Num. residues----131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031047
X-RAY DIFFRACTIONf_angle_d0.7651427
X-RAY DIFFRACTIONf_chiral_restr0.049161
X-RAY DIFFRACTIONf_plane_restr0.008187
X-RAY DIFFRACTIONf_dihedral_angle_d12.934653
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5014-2.63320.39981480.211216100
2.6332-2.79810.38321400.21215100
2.7981-3.01410.40611360.211192100
3.0141-3.31710.32281240.211237100
3.3171-3.79660.31891370.211230100
3.7966-4.7810.22391430.19911213100
4.781-100.21171320.1639121699

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