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- PDB-5l7z: Structure of Exuperantia EXO-like domain -

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Basic information

Entry
Database: PDB / ID: 5l7z
TitleStructure of Exuperantia EXO-like domain
ComponentsMaternal protein exuperantia
KeywordsRNA BINDING PROTEIN / Exonuclease / RNA / pseudo nuclease / hydrolase
Function / homology
Function and homology information


ovarian nurse cell to oocyte transport / bicoid mRNA localization / embryonic development via the syncytial blastoderm / 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 / bicoid mRNA localization / embryonic development via the syncytial blastoderm / 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 / Exuperantia RNAse H-like domain / Ribonuclease H superfamily
Similarity search - Domain/homology
Maternal protein exuperantia
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.37 Å
AuthorsLazzaretti, D. / Veith, K. / Bono, F.
Funding support Germany, 2items
OrganizationGrant numberCountry
ERC (FP7/2007-2013)310957 Germany
German Research FoundationBO3588/2-1 Germany
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 1.3May 8, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maternal protein exuperantia


Theoretical massNumber of molelcules
Total (without water)36,6291
Polymers36,6291
Non-polymers00
Water1,20767
1
A: Maternal protein exuperantia

A: Maternal protein exuperantia


Theoretical massNumber of molelcules
Total (without water)73,2572
Polymers73,2572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area1820 Å2
ΔGint-12 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.890, 79.890, 237.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Maternal protein exuperantia


Mass: 36628.590 Da / Num. of mol.: 1
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.: 67 / 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: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MPD, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.980, 1.040, 1.0
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 21, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
21.041
311
ReflectionResolution: 2.37→50 Å / Num. obs: 19097 / % possible obs: 100 % / Redundancy: 19 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 23.98
Reflection shellResolution: 2.37→2.47 Å / Rmerge(I) obs: 0.972 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.37→45.034 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.08
RfactorNum. reflection% reflection
Rfree0.2236 955 5 %
Rwork0.2042 --
obs0.2052 19097 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.37→45.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 0 67 1877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021841
X-RAY DIFFRACTIONf_angle_d0.4682494
X-RAY DIFFRACTIONf_dihedral_angle_d9.5291122
X-RAY DIFFRACTIONf_chiral_restr0.041291
X-RAY DIFFRACTIONf_plane_restr0.002319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3701-2.4950.29411320.25942521X-RAY DIFFRACTION100
2.495-2.65130.22661330.23942518X-RAY DIFFRACTION100
2.6513-2.8560.28571340.22282544X-RAY DIFFRACTION100
2.856-3.14340.25051330.22712542X-RAY DIFFRACTION100
3.1434-3.59810.26361360.22122571X-RAY DIFFRACTION100
3.5981-4.53250.20281380.17412630X-RAY DIFFRACTION100
4.5325-45.04170.19481490.19682816X-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)
14.56210.037-1.56993.4459-0.17892.84280.0825-0.1666-0.11910.0492-0.0092-0.19720.04960.0293-0.05540.366-0.0215-00.488-0.1790.4224-26.0373-30.11519.7954
24.2127-0.6256-2.62572.05260.43212.7810.1283-0.08490.11420.14760.0369-0.1784-0.15080.1786-0.09130.3598-0.0421-0.00150.4674-0.13350.3949-22.8168-27.381111.7024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 322 )

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