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- PDB-5a48: Crystal structure of the LOTUS domain (aa 139-240) of Drosophila ... -

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Basic information

Entry
Database: PDB / ID: 5a48
TitleCrystal structure of the LOTUS domain (aa 139-240) of Drosophila Oskar in P65
ComponentsMATERNAL EFFECT PROTEIN OSKAR
KeywordsPROTEIN BINDING / OST-HTH DOMAIN / WINGED HELIX-TURN-HELIX / DIMER / VASA INTERACTION / GERM PLASM
Function / homology
Function and homology information


posterior abdomen determination / pole plasm mRNA localization / regulation of oskar mRNA translation / P granule assembly / pole plasm protein localization / oocyte microtubule cytoskeleton polarization / pole plasm / posterior cell cortex / thermosensory behavior / P granule organization ...posterior abdomen determination / pole plasm mRNA localization / regulation of oskar mRNA translation / P granule assembly / pole plasm protein localization / oocyte microtubule cytoskeleton polarization / pole plasm / posterior cell cortex / thermosensory behavior / P granule organization / pole plasm assembly / segmentation / pole cell formation / visual behavior / P granule / germ cell nucleus / cortical actin cytoskeleton organization / oogenesis / germ cell development / protein localization to nucleus / long-term memory / regulation of mRNA stability / visual learning / cell cortex / endosome / mRNA binding / cytoplasm
Similarity search - Function
OSK domain / OSK domain / LOTUS domain-like / OST-HTH/LOTUS domain / LOTUS-like domain / OST-HTH/LOTUS domain / OST-type HTH domain profile. / SGNH hydrolase superfamily / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Maternal effect protein oskar
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsJeske, M. / Glatt, S. / Ephrussi, A. / Mueller, C.W.
CitationJournal: Cell Rep. / Year: 2015
Title: The Crystal Structure of the Drosophila Germline Inducer Oskar Identifies Two Domains with Distinct Vasa Helicase-and RNA-Binding Activities.
Authors: Jeske, M. / Bordi, M. / Glatt, S. / Muller, S. / Rybin, V. / Muller, C.W. / Ephrussi, A.
History
DepositionJun 5, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MATERNAL EFFECT PROTEIN OSKAR
B: MATERNAL EFFECT PROTEIN OSKAR


Theoretical massNumber of molelcules
Total (without water)23,4022
Polymers23,4022
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-0.6 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.160, 53.160, 109.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein MATERNAL EFFECT PROTEIN OSKAR


Mass: 11701.236 Da / Num. of mol.: 2 / Fragment: LOTUS DOMAIN, RESIDUES 139-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P25158
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.82 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 7333 / % possible obs: 99.9 % / Observed criterion σ(I): 1.49 / Redundancy: 11.4 % / Biso Wilson estimate: 41.62 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 9.66

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→46.038 Å / SU ML: 0.31 / σ(F): 2.36 / Phase error: 30.22 / Stereochemistry target values: ML
Details: THE OCCUPANCY OF SIDE CHAIN ATOMS, FOR WHICH ELECTRON DENSITY WAS POOR, IS SET TO 0.
RfactorNum. reflection% reflection
Rfree0.2338 368 5 %
Rwork0.1858 --
obs0.1882 7330 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→46.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 0 0 68 1461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041448
X-RAY DIFFRACTIONf_angle_d0.711964
X-RAY DIFFRACTIONf_dihedral_angle_d12.811542
X-RAY DIFFRACTIONf_chiral_restr0.05233
X-RAY DIFFRACTIONf_plane_restr0.002251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3505-2.69060.31331240.24762295X-RAY DIFFRACTION99
2.6906-3.38970.24951230.20112318X-RAY DIFFRACTION100
3.3897-46.04670.20621210.16452349X-RAY DIFFRACTION100

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