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- PDB-7yw5: Crystal Structure of the ITS1 processing by human ribonuclease IS... -

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Basic information

Entry
Database: PDB / ID: 7yw5
TitleCrystal Structure of the ITS1 processing by human ribonuclease ISG20L2 with mutation D327A
ComponentsInterferon-stimulated 20 kDa exonuclease-like 2
KeywordsRIBOSOMAL PROTEIN / ribonuclease
Function / homology
Function and homology information


exonuclease activity / Major pathway of rRNA processing in the nucleolus and cytosol / ribosome biogenesis / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / nucleolus / RNA binding / nucleus
Similarity search - Function
ISG20, DEDDh 3'-5' exonuclease domain / : / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Interferon-stimulated 20 kDa exonuclease-like 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsYang, X.Y. / Liu, X.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA.
Authors: Ma, Y. / Wang, J. / He, X. / Liu, Y. / Zhen, S. / An, L. / Yang, Q. / Niu, F. / Wang, H. / An, B. / Tai, X. / Yan, Z. / Wu, C. / Yang, X. / Liu, X.
History
DepositionAug 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon-stimulated 20 kDa exonuclease-like 2
B: Interferon-stimulated 20 kDa exonuclease-like 2


Theoretical massNumber of molelcules
Total (without water)43,5682
Polymers43,5682
Non-polymers00
Water43224
1
A: Interferon-stimulated 20 kDa exonuclease-like 2


Theoretical massNumber of molelcules
Total (without water)21,7841
Polymers21,7841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interferon-stimulated 20 kDa exonuclease-like 2


Theoretical massNumber of molelcules
Total (without water)21,7841
Polymers21,7841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.018, 59.017, 111.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Interferon-stimulated 20 kDa exonuclease-like 2


Mass: 21784.094 Da / Num. of mol.: 2 / Mutation: D327A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISG20L2, HSD-38, HSD38 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H9L3, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M BIS-TRIS propane pH9.0 30% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.49
ReflectionResolution: 2.77→52.14 Å / Num. obs: 17433 / % possible obs: 91.6 % / Redundancy: 2.349 % / CC1/2: 0.987 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.089 / Χ2: 1.061 / Net I/σ(I): 9.81 / Num. measured all: 40942
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.77-2.852.3060.2583.352972140412890.8910.32691.8
2.85-2.922.370.1914.53100138813080.9260.2494.2
2.92-3.012.3380.1525.692946133412600.9490.19294.5
3.01-3.12.3330.1276.382765130911850.9650.1690.5
3.1-3.22.2260.1037.782462123811060.9710.13289.3
3.2-3.322.2310.0848.712541123811390.9760.10792
3.32-3.442.4250.07810.182604114410740.9820.09893.9
3.44-3.582.4070.07710.992544114410570.9790.09792.4
3.58-3.742.4060.06811.61240110779980.9830.08692.7
3.74-3.922.3990.06912.25227710299490.9820.08792.2
3.92-4.142.3680.06312.6121159758930.9860.07991.6
4.14-4.392.3530.06413.119519368290.9860.08188.6
4.39-4.692.2340.06513.3516918707570.9810.08487
4.69-5.072.2910.06213.217468257620.9820.07992.4
5.07-5.552.4550.06613.7116997496920.9810.08392.4
5.55-6.22.4660.06513.6314976616070.9830.08191.8
6.2-7.162.4110.0713.8613216045480.9830.08790.7
7.16-8.772.330.05814.0710234984390.9890.07488.2
8.77-12.412.3690.06314.878223913470.9790.08188.7
12.41-52.142.3970.06914.444652111940.9880.08591.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wlj

1wlj


Resolution: 2.77→52.14 Å / Cross valid method: THROUGHOUT / σ(F): 40.89 / Phase error: 29.98 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2687 511 5.1 %
Rwork0.2585 --
obs0.2616 17433 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.77→52.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 0 0 24 2573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072605
X-RAY DIFFRACTIONf_angle_d0.8763525
X-RAY DIFFRACTIONf_dihedral_angle_d18.637967
X-RAY DIFFRACTIONf_chiral_restr0.053402
X-RAY DIFFRACTIONf_plane_restr0.007443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-3.050.46191230.43722347X-RAY DIFFRACTION93
3.05-3.50.31641250.31092366X-RAY DIFFRACTION93
3.5-4.40.28551240.24562373X-RAY DIFFRACTION93
4.41-52.140.19691290.21712434X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 12.3809 Å / Origin y: 1.7955 Å / Origin z: -13.9866 Å
111213212223313233
T0.3653 Å20.0474 Å20.0028 Å2-0.3448 Å20.0177 Å2--0.4796 Å2
L2.2849 °2-0.4783 °2-0.3156 °2-2.1963 °2-0.6144 °2--2.2178 °2
S0.1083 Å °-0.2626 Å °-0.0833 Å °-0.228 Å °0.0832 Å °-0.0968 Å °-0.146 Å °-0.2967 Å °-0.1945 Å °
Refinement TLS groupSelection details: all

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