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- PDB-5aoy: Structure of mouse Endonuclease V -

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Basic information

Entry
Database: PDB / ID: 5aoy
TitleStructure of mouse Endonuclease V
ComponentsENDONUCLEASE V
KeywordsHYDROLASE / ENDONUCLEASE / ENDONUCLEASE V
Function / homology
Function and homology information


DNA endonuclease activity, producing 5'-phosphomonoesters / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / cytoplasmic stress granule / single-stranded RNA binding / DNA repair / nucleolus / magnesium ion binding / DNA binding / cytoplasm
Similarity search - Function
Endonuclease V / Endonuclease V / archaeoglobus fulgidus dsm 4304 fold / archaeoglobus fulgidus dsm 4304 superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVik, E.S. / Nawaz, M.S. / Ronander, M.E. / Solvoll, A.M. / Strom-Andersen, P. / Bjoras, M. / Alseth, I. / Dalhus, B.
CitationJournal: Sci.Rep. / Year: 2016
Title: Crystal Structure and Md Simulation of Mouse Endov Reveal Wedge Motif Plasticity in This Inosine-Specific Endonuclease.
Authors: Nawaz, M.S. / Vik, E.S. / Ronander, M.E. / Solvoll, A.M. / Blicher, P. / Bjoras, M. / Alseth, I. / Dalhus, B.
History
DepositionSep 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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: ENDONUCLEASE V


Theoretical massNumber of molelcules
Total (without water)27,7061
Polymers27,7061
Non-polymers00
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.630, 114.030, 54.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2008-

HOH

21A-2029-

HOH

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Components

#1: Protein ENDONUCLEASE V


Mass: 27706.111 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PETM41 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RIPL
References: UniProt: Q8C9A2, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.8 Å3/Da / Density % sol: 55 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.75→32.47 Å / Num. obs: 32035 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B20

4b20


Resolution: 1.75→32.474 Å / SU ML: 0.1 / σ(F): 0.03 / Phase error: 16.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1903 1598 5.1 %
Rwork0.1649 --
obs0.1661 31483 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.3 Å2
Refinement stepCycle: LAST / Resolution: 1.75→32.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 0 302 2158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071938
X-RAY DIFFRACTIONf_angle_d1.1942631
X-RAY DIFFRACTIONf_dihedral_angle_d14.956737
X-RAY DIFFRACTIONf_chiral_restr0.08300
X-RAY DIFFRACTIONf_plane_restr0.01342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80650.24711380.21712581X-RAY DIFFRACTION95
1.8065-1.87110.19151270.19082637X-RAY DIFFRACTION96
1.8711-1.9460.22151530.17832648X-RAY DIFFRACTION97
1.946-2.03450.2191360.16622689X-RAY DIFFRACTION98
2.0345-2.14180.19431430.1552696X-RAY DIFFRACTION99
2.1418-2.27590.20421450.15772716X-RAY DIFFRACTION99
2.2759-2.45160.18281490.16552750X-RAY DIFFRACTION99
2.4516-2.69820.20061680.16452706X-RAY DIFFRACTION99
2.6982-3.08840.19471410.16342768X-RAY DIFFRACTION99
3.0884-3.890.17121570.1472795X-RAY DIFFRACTION100
3.89-32.47950.16211410.16542899X-RAY DIFFRACTION99

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