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- PDB-7jw2: Crystal structure of Aedes aegypti Nibbler EXO domain -

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Basic information

Entry
Database: PDB / ID: 7jw2
TitleCrystal structure of Aedes aegypti Nibbler EXO domain
ComponentsExonuclease mut-7 homolog
KeywordsRNA BINDING PROTEIN / Nibbler / exoribonuclease / microRNA trimming / piRNA trimming
Function / homology
Function and homology information


nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / nucleic acid binding / Hydrolases; Acting on ester bonds / metal ion binding
Similarity search - Function
Exonuclease Mut-7, DEDDy 3'-5' exonuclease domain / : / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Exonuclease mut-7 homolog
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsXie, W. / Sowemimo, I. / Hayashi, R. / Wang, J. / Brennecke, J. / Ameres, S.L. / Patel, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structure-function analysis of microRNA 3'-end trimming by Nibbler.
Authors: Xie, W. / Sowemimo, I. / Hayashi, R. / Wang, J. / Burkard, T.R. / Brennecke, J. / Ameres, S.L. / Patel, D.J.
History
DepositionAug 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exonuclease mut-7 homolog
B: Exonuclease mut-7 homolog


Theoretical massNumber of molelcules
Total (without water)52,2592
Polymers52,2592
Non-polymers00
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-9 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.508, 71.584, 83.031
Angle α, β, γ (deg.)90.000, 97.320, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Exonuclease mut-7 homolog / Exonuclease 3'-5' domain-containing protein 3 homolog


Mass: 26129.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: AAEL005527 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q179T2, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium formate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→37.28 Å / Num. obs: 72680 / % possible obs: 98.85 % / Redundancy: 4.5 % / Biso Wilson estimate: 18.39 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.03341 / Rpim(I) all: 0.01727 / Rrim(I) all: 0.03775 / Net I/σ(I): 26.22
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.1528 / Mean I/σ(I) obs: 5.74 / Num. unique obs: 6711 / CC1/2: 0.983 / CC star: 0.996 / Rpim(I) all: 0.09235 / Rrim(I) all: 0.1796 / % possible all: 91.92

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Drosophila Nbr EXO domain

Resolution: 1.5→37.28 Å / SU ML: 0.1501 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.9256
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2074 3628 5 %
Rwork0.1916 68941 -
obs0.1924 72569 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 0 425 3977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00563632
X-RAY DIFFRACTIONf_angle_d0.79794925
X-RAY DIFFRACTIONf_chiral_restr0.0504549
X-RAY DIFFRACTIONf_plane_restr0.0046632
X-RAY DIFFRACTIONf_dihedral_angle_d5.6868467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.26811400.22352336X-RAY DIFFRACTION86.66
1.52-1.540.26221350.21622427X-RAY DIFFRACTION93.23
1.54-1.560.23311300.21172648X-RAY DIFFRACTION98.9
1.56-1.590.26061390.21312690X-RAY DIFFRACTION99.79
1.59-1.610.22781410.20942658X-RAY DIFFRACTION99.86
1.61-1.640.26951510.21332677X-RAY DIFFRACTION99.79
1.64-1.670.22711480.20642652X-RAY DIFFRACTION99.89
1.67-1.70.27541200.21462647X-RAY DIFFRACTION99.75
1.7-1.730.26591560.21042680X-RAY DIFFRACTION99.86
1.73-1.760.22881350.20772684X-RAY DIFFRACTION99.89
1.76-1.80.23081540.21372652X-RAY DIFFRACTION99.72
1.8-1.840.23271200.20732668X-RAY DIFFRACTION99.61
1.84-1.890.20781310.20552693X-RAY DIFFRACTION99.65
1.89-1.940.20891310.20872662X-RAY DIFFRACTION99.79
1.94-20.23891390.20762686X-RAY DIFFRACTION99.86
2-2.060.24181440.20892669X-RAY DIFFRACTION99.93
2.06-2.140.2181270.20442676X-RAY DIFFRACTION99.82
2.14-2.220.22431440.19862680X-RAY DIFFRACTION99.75
2.22-2.320.21821180.1932705X-RAY DIFFRACTION99.54
2.32-2.450.23331260.20812671X-RAY DIFFRACTION99.5
2.45-2.60.23031520.2042660X-RAY DIFFRACTION99.5
2.6-2.80.24271660.19262646X-RAY DIFFRACTION99.01
2.8-3.080.19621410.19942677X-RAY DIFFRACTION99.47
3.08-3.530.19361470.18162687X-RAY DIFFRACTION99.61
3.53-4.440.16491350.15952709X-RAY DIFFRACTION99.51
4.44-37.280.16291580.17192701X-RAY DIFFRACTION98.52

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