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- PDB-8wxs: Crystal structure of the LOTUS domain of Drosophila Tejas -

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Basic information

Entry
Database: PDB / ID: 8wxs
TitleCrystal structure of the LOTUS domain of Drosophila Tejas
ComponentsFI02030p
KeywordsRNA BINDING PROTEIN / piRNA / Tudor domain-containing protein
Function / homology
Function and homology information


P granule organization / transposable element silencing by mRNA destabilization / secondary piRNA processing / piRNA processing / P granule / spermatogenesis
Similarity search - Function
OST-HTH/LOTUS domain / LOTUS-like domain / OST-HTH/LOTUS domain / OST-type HTH domain profile. / : / Tudor domain / Tudor domain / SNase-like, OB-fold superfamily
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHuang, Y. / Zhang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171186 China
National Natural Science Foundation of China (NSFC)31870741 China
CitationJournal: To Be Published
Title: Crystal structure of the LOTUS domain of Drosophila Tejas
Authors: Huang, Y. / Zhang, Y.
History
DepositionOct 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FI02030p
B: FI02030p


Theoretical massNumber of molelcules
Total (without water)17,1022
Polymers17,1022
Non-polymers00
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.645, 36.645, 235.485
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein FI02030p / Tejas LOTUS


Mass: 8550.815 Da / Num. of mol.: 2 / Mutation: E37A, E38A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: tej / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1Z9P1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NH4Ac, 0.1 M NaAc, pH 4.6, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97928 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 11648 / % possible obs: 98.5 % / Redundancy: 9.6 % / Biso Wilson estimate: 21.26 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 54.89
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.13 / Num. unique obs: 1022

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.92 Å / SU ML: 0.1472 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.8789
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2228 1164 9.99 %
Rwork0.1864 10484 -
obs0.19 11648 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.97 Å2
Refinement stepCycle: LAST / Resolution: 2→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 0 0 189 1318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311148
X-RAY DIFFRACTIONf_angle_d0.69461555
X-RAY DIFFRACTIONf_chiral_restr0.0428189
X-RAY DIFFRACTIONf_plane_restr0.0061191
X-RAY DIFFRACTIONf_dihedral_angle_d5.0112158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.24481290.20421163X-RAY DIFFRACTION92.02
2.09-2.20.25931430.19121279X-RAY DIFFRACTION99.44
2.2-2.340.21151420.18171292X-RAY DIFFRACTION99.93
2.34-2.520.19351450.18371302X-RAY DIFFRACTION100
2.52-2.770.23421460.19191308X-RAY DIFFRACTION100
2.77-3.170.2291470.20341333X-RAY DIFFRACTION99.93
3.17-3.990.23871510.16581359X-RAY DIFFRACTION99.6
4-28.920.20071610.19011448X-RAY DIFFRACTION97.69

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