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- PDB-9jxw: Crystal structure of SiRe_0806 from Sulfolobus islandicus -

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Basic information

Entry
Database: PDB / ID: 9jxw
TitleCrystal structure of SiRe_0806 from Sulfolobus islandicus
ComponentsPIN domain-containing protein
KeywordsIMMUNE SYSTEM / Sulfolobus islandicus / SiRe_0806 / cyclic oligo-adenylates (cOAs) / CARF domain / PIN domain / RNase
Function / homologyPIN domain-containing protein
Function and homology information
Biological speciesSulfolobus islandicus REY15A (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWang, F. / Zhao, P. / Bi, X. / She, Q.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0906800 China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Cyclic tetraadenylate binding induces dimerization of protein dimers to activate a CRISPR-associated PIN nuclease.
Authors: Wang, F. / Zhao, P. / Bi, X. / Zheng, R. / Tian, X. / Xu, J. / Jiang, S. / Li, G. / Shen, Y. / She, Q.
History
DepositionOct 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PIN domain-containing protein
B: PIN domain-containing protein


Theoretical massNumber of molelcules
Total (without water)99,0012
Polymers99,0012
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-13 kcal/mol
Surface area36210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.929, 95.623, 108.822
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 PIN domain-containing protein


Mass: 49500.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Author remarks: Amino acids 1-417 correspond to the SiRe_0806 protein (UNP F0NH84), amino acids 418-423 constitute the linker connecting the SiRe_0806 protein to the C-terminal His-tag, and ...Details: Author remarks: Amino acids 1-417 correspond to the SiRe_0806 protein (UNP F0NH84), amino acids 418-423 constitute the linker connecting the SiRe_0806 protein to the C-terminal His-tag, and amino acids 424-429 represent the His-tag.
Source: (gene. exp.) Sulfolobus islandicus REY15A (archaea) / Strain: REY15A / Gene: SiRe_0806 / Production host: Sulfolobus islandicus REY15A (archaea) / References: UniProt: F0NH84
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

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate trihydrate, pH=4.76; 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→43.77 Å / Num. obs: 18726 / % possible obs: 99.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.4
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 0.309 / Num. unique obs: 2991

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→43.77 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2947 951 5.1 %
Rwork0.2644 --
obs0.266 18654 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 0 0 6624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026725
X-RAY DIFFRACTIONf_angle_d0.5539056
X-RAY DIFFRACTIONf_dihedral_angle_d12.2572588
X-RAY DIFFRACTIONf_chiral_restr0.0421027
X-RAY DIFFRACTIONf_plane_restr0.0041152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.160.44261370.35192482X-RAY DIFFRACTION100
3.16-3.360.3821330.32112479X-RAY DIFFRACTION100
3.36-3.610.36741110.32562531X-RAY DIFFRACTION100
3.61-3.980.29751300.27282505X-RAY DIFFRACTION99
3.98-4.550.30331270.2582543X-RAY DIFFRACTION100
4.55-5.730.25751530.24762518X-RAY DIFFRACTION99
5.74-43.770.27841600.24552645X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.53380.34520.87653.4562.93082.7055-0.10640.30050.4672-0.0418-0.22580.46110.0106-0.29320.32980.7782-0.070.02680.78850.26080.843414.92998.223318.1115
21.07440.95840.54032.0792.05813.4276-0.17810.4166-0.6735-0.72770.6905-1.0897-0.36320.5589-0.51951.0332-0.20320.40370.7707-0.1751.547948.72895.850916.3215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 420)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 418)

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