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- PDB-7jw3: Crystal structure of Aedes aegypti Nibbler NTD domain -

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Basic information

Entry
Database: PDB / ID: 7jw3
TitleCrystal structure of Aedes aegypti Nibbler NTD domain
ComponentsExonuclease mut-7 homolog
KeywordsRNA BINDING PROTEIN / Nibbler / exoribonuclease / microRNA trimming / piRNA trimming / HEAT
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 superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Exonuclease mut-7 homolog
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.05 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 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)136,8713
Polymers136,8713
Non-polymers00
Water00
1
C: Exonuclease mut-7 homolog


Theoretical massNumber of molelcules
Total (without water)45,6241
Polymers45,6241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Exonuclease mut-7 homolog


Theoretical massNumber of molelcules
Total (without water)45,6241
Polymers45,6241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Exonuclease mut-7 homolog


Theoretical massNumber of molelcules
Total (without water)45,6241
Polymers45,6241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)219.224, 219.224, 39.382
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z

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Components

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


Mass: 45623.625 Da / Num. of mol.: 3
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
Has ligand of interestN
Has protein modificationY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M sodium tartrate, 0.1 M HEPES, pH 7.0, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.05→30 Å / Num. obs: 21285 / % possible obs: 99.73 % / Redundancy: 20.2 % / Biso Wilson estimate: 114.23 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1599 / Rpim(I) all: 0.03625 / Rrim(I) all: 0.164 / Net I/σ(I): 18.12
Reflection shellResolution: 3.05→3.159 Å / Redundancy: 20.1 % / Rmerge(I) obs: 3.551 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 2058 / CC1/2: 0.524 / CC star: 0.829 / Rpim(I) all: 0.8052 / Rrim(I) all: 3.642 / % possible all: 99.28

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.05→29.21 Å / SU ML: 0.4802 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.5035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2669 1039 4.89 %
Rwork0.2357 20229 -
obs0.2373 21268 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 125.41 Å2
Refinement stepCycle: LAST / Resolution: 3.05→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6113 0 0 0 6113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00276261
X-RAY DIFFRACTIONf_angle_d0.61038431
X-RAY DIFFRACTIONf_chiral_restr0.0428880
X-RAY DIFFRACTIONf_plane_restr0.00431100
X-RAY DIFFRACTIONf_dihedral_angle_d19.08392371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.210.39311480.35072801X-RAY DIFFRACTION99.49
3.21-3.410.35961600.32112831X-RAY DIFFRACTION99.97
3.41-3.670.33021800.29742837X-RAY DIFFRACTION99.97
3.68-4.040.25221280.2492898X-RAY DIFFRACTION100
4.04-4.630.25571390.22152887X-RAY DIFFRACTION100
4.63-5.820.25491500.23952918X-RAY DIFFRACTION100
5.82-29.210.24241340.20273057X-RAY DIFFRACTION99.87

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