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- PDB-4ro1: An 3'-5'-exoribonuclease that specifically recognizes RNAs. -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4ro1
TitleAn 3'-5'-exoribonuclease that specifically recognizes RNAs.
ComponentsDIS3-like exonuclease 2
KeywordsHYDROLASE / OB-folds and RNB / RNA digestion
Function / homology
Function and homology information


polyuridylation-dependent mRNA catabolic process / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process / P-body / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / metal ion binding / cytosol / cytoplasm
Similarity search - Function
DIS3-like exonuclease 2-like, C-terminal / DIS3-like exonuclease 2 / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain / RNB / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DIS3-like exonuclease 2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.803 Å
AuthorsLv, H. / Zhu, Y. / Teng, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural analysis of Dis3l2, an exosome-independent exonuclease from Schizosaccharomyces pombe.
Authors: Lv, H. / Zhu, Y. / Qiu, Y. / Niu, L. / Teng, M. / Li, X.
History
DepositionOct 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DIS3-like exonuclease 2
A: DIS3-like exonuclease 2


Theoretical massNumber of molelcules
Total (without water)174,1312
Polymers174,1312
Non-polymers00
Water00
1
A: DIS3-like exonuclease 2


Theoretical massNumber of molelcules
Total (without water)87,0661
Polymers87,0661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DIS3-like exonuclease 2


Theoretical massNumber of molelcules
Total (without water)87,0661
Polymers87,0661
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.966, 54.201, 127.217
Angle α, β, γ (deg.)90.00, 107.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DIS3-like exonuclease 2


Mass: 87065.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: dis32, dis3l2, SPAC2C4.07c / Production host: Escherichia coli (E. coli)
References: UniProt: O14040, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters

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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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 4000, 0.15M (NH4)2SO4, 0.1M HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.9791 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→121.6 Å / Num. obs: 37850 / % possible obs: 99.8 % / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
HKL-2000data collection
AutoSolphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.803→40.532 Å / SU ML: 0.36 / σ(F): 1.35 / Phase error: 33.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2936 1888 4.99 %
Rwork0.2685 --
obs0.2697 37847 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.803→40.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8275 0 0 0 8275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048475
X-RAY DIFFRACTIONf_angle_d1.00511562
X-RAY DIFFRACTIONf_dihedral_angle_d15.2982844
X-RAY DIFFRACTIONf_chiral_restr0.0351335
X-RAY DIFFRACTIONf_plane_restr0.0071507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8033-2.8790.38241440.31992661X-RAY DIFFRACTION97
2.879-2.96370.34541290.30092747X-RAY DIFFRACTION99
2.9637-3.05940.33941370.29892720X-RAY DIFFRACTION100
3.0594-3.16870.34451330.28292802X-RAY DIFFRACTION99
3.1687-3.29550.27061360.2842733X-RAY DIFFRACTION100
3.2955-3.44540.29271450.27742766X-RAY DIFFRACTION100
3.4454-3.62690.27641470.26892776X-RAY DIFFRACTION100
3.6269-3.8540.29711260.2642768X-RAY DIFFRACTION100
3.854-4.15130.28491730.25232750X-RAY DIFFRACTION100
4.1513-4.56860.22931390.24572780X-RAY DIFFRACTION100
4.5686-5.22850.28011610.24932752X-RAY DIFFRACTION100
5.2285-6.58270.33491730.28942796X-RAY DIFFRACTION100
6.5827-40.53630.28721450.25982908X-RAY DIFFRACTION99

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