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- PDB-7jw6: Crystal structure of Drosophila Nibbler EXO domain -

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Basic information

Entry
Database: PDB / ID: 7jw6
TitleCrystal structure of Drosophila Nibbler EXO domain
ComponentsExonuclease mut-7 homolog
KeywordsRNA BINDING PROTEIN / Nibbler / exoribonuclease / microRNA trimming / piRNA trimming / HEAT
Function / homology
Function and homology information


pre-miRNA 3'-end processing / 3'-5'-exoribonuclease activity involved in mature miRNA 3'-end processing / primary piRNA processing / secondary piRNA processing / piRNA processing / transposable element silencing / miRNA processing / P granule / 3'-5' exonuclease activity / 3'-5'-RNA exonuclease activity ...pre-miRNA 3'-end processing / 3'-5'-exoribonuclease activity involved in mature miRNA 3'-end processing / primary piRNA processing / secondary piRNA processing / piRNA processing / transposable element silencing / miRNA processing / P granule / 3'-5' exonuclease activity / 3'-5'-RNA exonuclease activity / nucleic acid binding / Hydrolases; Acting on ester bonds / ribonucleoprotein complex / metal ion binding / nucleus / cytoplasm
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 speciesDrosophila melanogaster (fruit fly)
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

Downloads & links

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Assembly

Deposited unit
A: Exonuclease mut-7 homolog


Theoretical massNumber of molelcules
Total (without water)26,7031
Polymers26,7031
Non-polymers00
Water4,450247
1
A: Exonuclease mut-7 homolog

A: Exonuclease mut-7 homolog


Theoretical massNumber of molelcules
Total (without water)53,4062
Polymers53,4062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area2920 Å2
ΔGint-14 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.338, 117.101, 87.481
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-710-

HOH

21A-741-

HOH

31A-909-

HOH

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Components

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


Mass: 26703.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Nbr, CG9247 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9VIF1, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.064 M sodium citrate 7.0, 0.1 M HEPES, pH 7.0, 10% PEG5000MME

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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: 1.5→29.3 Å / Num. obs: 36858 / % possible obs: 97.49 % / Redundancy: 13.1 % / Biso Wilson estimate: 17.74 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1678 / Rpim(I) all: 0.04813 / Rrim(I) all: 0.1748 / Net I/σ(I): 15.06
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.262 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3620 / CC1/2: 0.713 / CC star: 0.912 / Rpim(I) all: 0.3584 / Rrim(I) all: 1.313 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model from SAD

Resolution: 1.5→29.3 Å / SU ML: 0.2222 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4227
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2317 1712 4.76 %
Rwork0.2018 34271 -
obs0.2032 35983 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 0 247 2074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541893
X-RAY DIFFRACTIONf_angle_d0.75442565
X-RAY DIFFRACTIONf_chiral_restr0.0515290
X-RAY DIFFRACTIONf_plane_restr0.0044330
X-RAY DIFFRACTIONf_dihedral_angle_d20.6735724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.33891300.31922883X-RAY DIFFRACTION99.93
1.54-1.590.30831430.28462896X-RAY DIFFRACTION99.9
1.59-1.650.27181440.25362888X-RAY DIFFRACTION99.97
1.65-1.720.23231440.20252899X-RAY DIFFRACTION99.84
1.72-1.80.23771480.19032888X-RAY DIFFRACTION100
1.8-1.890.27681520.2312760X-RAY DIFFRACTION95.16
1.89-2.010.3421210.30112461X-RAY DIFFRACTION84.46
2.01-2.160.20091710.1842886X-RAY DIFFRACTION99.97
2.16-2.380.26151180.23452706X-RAY DIFFRACTION91.96
2.38-2.720.22761440.1912960X-RAY DIFFRACTION99.71
2.73-3.430.1971510.17732953X-RAY DIFFRACTION100
3.43-29.30.19811460.16453091X-RAY DIFFRACTION99.11

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