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- PDB-5a4a: Crystal structure of the OSK domain of Drosophila Oskar -

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Basic information

Entry
Database: PDB / ID: 5a4a
TitleCrystal structure of the OSK domain of Drosophila Oskar
ComponentsMATERNAL EFFECT PROTEIN OSKAR
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / SGNH HYDROLASE / RNA BINDING / 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 / pole plasm assembly ...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 / pole plasm assembly / segmentation / P granule organization / 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 / OST-HTH/LOTUS domain / LOTUS-like domain / OST-HTH/LOTUS domain / OST-type HTH domain profile. / SGNH hydrolase / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Maternal effect protein oskar
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.699 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 1.3Aug 23, 2017Group: Data collection / Category: diffrn_detector / reflns / reflns_shell / Item: _diffrn_detector.type / _reflns.pdbx_CC_half
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MATERNAL EFFECT PROTEIN OSKAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7487
Polymers24,1711
Non-polymers5766
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.430, 68.430, 101.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein MATERNAL EFFECT PROTEIN OSKAR / OSKAR


Mass: 24171.199 Da / Num. of mol.: 1 / Fragment: OSK DOMAIN, RESIDUES 401-606
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.83 Å3/Da / Density % sol: 56.48 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99986
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 30657 / % possible obs: 99.7 % / Observed criterion σ(I): 1.51 / Redundancy: 9.9 % / Biso Wilson estimate: 18.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.16 / Net I/σ(I): 13.31
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.867 / Mean I/σ(I) obs: 1.51 / CC1/2: 0.64 / % possible all: 97.6

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.699→34.215 Å / SU ML: 0.17 / σ(F): 1.36 / Phase error: 19.38 / Stereochemistry target values: ML
Details: THE OCCUPANCY OF SIDE CHAIN ATOMS, FOR WHICH ELECTRON DENSITY WAS POOR, IS SET TO 0.
RfactorNum. reflection% reflection
Rfree0.1945 2384 7.8 %
Rwork0.1663 --
obs0.1685 30656 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.699→34.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 30 258 1966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071759
X-RAY DIFFRACTIONf_angle_d1.0462375
X-RAY DIFFRACTIONf_dihedral_angle_d13.118666
X-RAY DIFFRACTIONf_chiral_restr0.077260
X-RAY DIFFRACTIONf_plane_restr0.004301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6991-1.73380.26631310.29481600X-RAY DIFFRACTION97
1.7338-1.77150.34171420.27321618X-RAY DIFFRACTION99
1.7715-1.81270.29821360.25191635X-RAY DIFFRACTION99
1.8127-1.8580.29091390.22891634X-RAY DIFFRACTION99
1.858-1.90830.23631360.21261661X-RAY DIFFRACTION99
1.9083-1.96440.23791390.19661614X-RAY DIFFRACTION100
1.9644-2.02780.20661420.17981652X-RAY DIFFRACTION100
2.0278-2.10030.21021380.16471656X-RAY DIFFRACTION100
2.1003-2.18440.19651380.15331660X-RAY DIFFRACTION100
2.1844-2.28370.17171400.15351662X-RAY DIFFRACTION100
2.2837-2.40410.17321370.14541644X-RAY DIFFRACTION100
2.4041-2.55470.18951460.15131675X-RAY DIFFRACTION100
2.5547-2.75190.18461400.15621670X-RAY DIFFRACTION100
2.7519-3.02870.19461410.1611678X-RAY DIFFRACTION100
3.0287-3.46650.1741400.14751711X-RAY DIFFRACTION100
3.4665-4.36610.14741430.13311709X-RAY DIFFRACTION100
4.3661-34.22190.19431560.17391793X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.09790.14480.11021.1729-0.28841.58330.02960.03710.01260.00150.020.09540.0467-0.2957-0.06330.1120.0054-0.0020.1340.00650.092828.08419.697839.1085
21.32790.3918-0.06410.88780.15022.05020.02120.02080.1607-0.01240.03150.0476-0.27960.022-0.0420.11910.0014-0.00240.0549-0.00310.088438.759427.501149.7764
30.51940.1139-0.27270.32340.18191.6968-0.0039-0.0426-0.08310.05880.0421-0.10180.23380.254-0.05410.12950.038-0.02250.1277-0.0130.132244.640713.818846.7265
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 399 THROUGH 460 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 461 THROUGH 546 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 547 THROUGH 606 )

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