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- PDB-5l80: Structure of Exuperantia EXO-like and SAM-like domains -

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Basic information

Entry
Database: PDB / ID: 5l80
TitleStructure of Exuperantia EXO-like and SAM-like domains
ComponentsMaternal protein exuperantia,Maternal protein exuperantia
KeywordsRNA BINDING PROTEIN / Exonuclease / RNA / pseudo nuclease / SAM domain
Function / homology
Function and homology information


ovarian nurse cell to oocyte transport / embryonic development via the syncytial blastoderm / bicoid mRNA localization / regulation of pole plasm oskar mRNA localization / pole plasm oskar mRNA localization / anterior/posterior axis specification, embryo / precatalytic spliceosome / P-body / mRNA splicing, via spliceosome / cytoplasmic ribonucleoprotein granule ...ovarian nurse cell to oocyte transport / embryonic development via the syncytial blastoderm / bicoid mRNA localization / regulation of pole plasm oskar mRNA localization / pole plasm oskar mRNA localization / anterior/posterior axis specification, embryo / precatalytic spliceosome / P-body / mRNA splicing, via spliceosome / cytoplasmic ribonucleoprotein granule / spermatogenesis / single-stranded RNA binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Maternal protein exuperantia / Exuperantia, SAM-like domain / Exuperantia SAM-like domain / Ribonuclease H superfamily
Similarity search - Domain/homology
Maternal protein exuperantia
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLazzaretti, D. / Veith, K. / Bono, F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: The bicoid mRNA localization factor Exuperantia is an RNA-binding pseudonuclease.
Authors: Lazzaretti, D. / Veith, K. / Kramer, K. / Basquin, C. / Urlaub, H. / Irion, U. / Bono, F.
History
DepositionJun 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maternal protein exuperantia,Maternal protein exuperantia
B: Maternal protein exuperantia,Maternal protein exuperantia


Theoretical massNumber of molelcules
Total (without water)79,4012
Polymers79,4012
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-23 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.540, 66.590, 81.330
Angle α, β, γ (deg.)90.00, 113.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Maternal protein exuperantia,Maternal protein exuperantia


Mass: 39700.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: exu, CG8994 / Production host: Escherichia coli (E. coli) / References: UniProt: P28750
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: Sodium Malonate, PEG 1000, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 19360 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 19.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.045 / Mean I/σ(I) obs: 2.2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L7Z

5l7z


Resolution: 2.8→47.336 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.02
RfactorNum. reflection% reflection
Rfree0.2765 969 5.01 %
Rwork0.2523 --
obs0.2535 19360 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4229 0 0 11 4240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034294
X-RAY DIFFRACTIONf_angle_d0.6585823
X-RAY DIFFRACTIONf_dihedral_angle_d11.7411485
X-RAY DIFFRACTIONf_chiral_restr0.027693
X-RAY DIFFRACTIONf_plane_restr0.002743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94760.36761370.31452600X-RAY DIFFRACTION99
2.9476-3.13230.35431380.30652616X-RAY DIFFRACTION100
3.1323-3.37410.29471360.29742592X-RAY DIFFRACTION100
3.3741-3.71350.28441380.26312622X-RAY DIFFRACTION100
3.7135-4.25050.2741380.23352611X-RAY DIFFRACTION100
4.2505-5.3540.24531390.22432652X-RAY DIFFRACTION100
5.354-47.30.26551430.24792698X-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)
13.7696-0.5839-1.57276.56311.17515.4759-0.12-0.009-0.44270.35660.02340.54510.4809-0.23310.04340.45190.00860.03430.35440.04760.4713-25.5027-21.197-11.062
20.97220.1921-0.60291.392-2.29755.52550.4695-0.6938-0.79390.11990.0663-0.26470.4638-0.7855-0.18210.9197-0.1124-0.16050.90190.20520.9874-34.86185.7499-33.2847
31.4502-2.2631-0.30415.14222.52912.7174-0.0795-0.93890.09360.9976-0.08481.0225-1.2403-0.8514-0.3361.31430.1818-0.01220.97660.15240.9085-41.4918.7445-30.7237
44.68241.1299-0.34254.9491-1.01993.8267-0.0079-0.12820.00160.038-0.2233-0.7303-0.41851.06090.11910.6417-0.1462-0.01320.65950.05720.6491-3.50588.9962-18.8851
54.004-0.1891.40368.3511-1.01650.59961.04890.57041.0419-0.8727-0.457-0.711-0.887-1.80920.23441.58560.77750.04771.78810.00610.9395-15.35574.420115.7894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 268 )
2X-RAY DIFFRACTION2chain 'A' and (resid 269 through 329 )
3X-RAY DIFFRACTION3chain 'A' and (resid 330 through 344 )
4X-RAY DIFFRACTION4chain 'B' and (resid 28 through 261 )
5X-RAY DIFFRACTION5chain 'B' and (resid 262 through 343 )

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