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- PDB-5cd9: Crystal structure of the CTD of Drosophila Oskar protein -

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Basic information

Entry
Database: PDB / ID: 5cd9
TitleCrystal structure of the CTD of Drosophila Oskar protein
ComponentsMaternal effect protein oskar
KeywordsRNA BINDING PROTEIN / 3'-UTR / dimerization
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 / SAD / Resolution: 2.102 Å
AuthorsYang, N. / Hu, M. / Yu, Z. / Wang, M. / Lehmann, R. / Xu, R.M.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370734 China
National Natural Science Foundation of China31400670 China
MOST2015CB856202 China
National key New Drug Creation and Manufacturing Program2014ZX09507002 China
CASXDB08010100 China
CASKJZDEW-L05 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of Drosophila Oskar reveals a novel RNA binding protein
Authors: Yang, N. / Yu, Z. / Hu, M. / Wang, M. / Lehmann, R. / Xu, R.M.
History
DepositionJul 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation

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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)25,9768
Polymers25,3031
Non-polymers6727
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-20 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.999, 68.999, 100.687
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Maternal effect protein oskar


Mass: 25303.457 Da / Num. of mol.: 1 / Fragment: UNP residues 393-606
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: osk, CG10901 / Plasmid: pET28a-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: P25158
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.6 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 800mM (NH4)2SO4, 200mM LiSO4, 100mM NaAC pH4.6 / PH range: 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 16668 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.69 Å2 / Rmerge(I) obs: 0.115 / Χ2: 1.21 / Net I/av σ(I): 11.741 / Net I/σ(I): 8.7 / Num. measured all: 64051
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.1-2.183.90.423316341.02399.9
2.18-2.263.90.35716351.02499.8
2.26-2.373.90.29516411.10799.8
2.37-2.493.90.25616481.1499.9
2.49-2.653.90.20616461.25499.8
2.65-2.853.90.16516481.3299.9
2.85-3.143.90.12716611.254100
3.14-3.593.80.09316731.18499.9
3.59-4.523.80.08416991.10699.9
4.52-503.60.06217831.70399.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.102→32.637 Å / FOM work R set: 0.8641 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.97 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 816 4.91 %Random selection
Rwork0.1613 15801 --
obs0.1633 16617 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.04 Å2 / Biso mean: 27.84 Å2 / Biso min: 14.82 Å2
Refinement stepCycle: final / Resolution: 2.102→32.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 35 241 1977
Biso mean--33.14 35.62 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051802
X-RAY DIFFRACTIONf_angle_d0.9342446
X-RAY DIFFRACTIONf_chiral_restr0.061273
X-RAY DIFFRACTIONf_plane_restr0.004308
X-RAY DIFFRACTIONf_dihedral_angle_d12.412696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1021-2.23380.24671440.20525682712
2.2338-2.40620.24081440.179825802724
2.4062-2.64830.24421370.169326102747
2.6483-3.03130.2241320.160926012733
3.0313-3.81810.17051250.140226812806
3.8181-32.64070.17851340.158527612895

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