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- PDB-8wje: Structure of apo-SPO1 Tad2 -

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Basic information

Entry
Database: PDB / ID: 8wje
TitleStructure of apo-SPO1 Tad2
ComponentsGp34.65
KeywordsVIRAL PROTEIN
Function / homologyProtein of unknown function DUF2829 / Thoeris anti-defense 2-like domain / metal ion binding / Thoeris anti-defense 2
Function and homology information
Biological speciesBacillus phage SPO1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsXiao, Y. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2024
Title: Single phage proteins sequester signals from TIR and cGAS-like enzymes.
Authors: Li, D. / Xiao, Y. / Fedorova, I. / Xiong, W. / Wang, Y. / Liu, X. / Huiting, E. / Ren, J. / Gao, Z. / Zhao, X. / Cao, X. / Zhang, Y. / Bondy-Denomy, J. / Feng, Y.
History
DepositionSep 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Dec 4, 2024Group: Data collection / Database references / Category: citation / citation_author / reflns_shell
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _reflns_shell.pdbx_Rrim_I_all

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Gp34.65
C: Gp34.65
D: Gp34.65
E: Gp34.65
F: Gp34.65
A: Gp34.65


Theoretical massNumber of molelcules
Total (without water)64,7246
Polymers64,7246
Non-polymers00
Water1,27971
1
B: Gp34.65
C: Gp34.65
D: Gp34.65
A: Gp34.65


Theoretical massNumber of molelcules
Total (without water)43,1494
Polymers43,1494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-46 kcal/mol
Surface area19140 Å2
MethodPISA
2
E: Gp34.65
F: Gp34.65

E: Gp34.65
F: Gp34.65


Theoretical massNumber of molelcules
Total (without water)43,1494
Polymers43,1494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6860 Å2
ΔGint-44 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.094, 69.108, 92.154
Angle α, β, γ (deg.)90.00, 95.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Gp34.65


Mass: 10787.275 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage SPO1 (virus) / Gene: 34.65 / Production host: Escherichia coli (E. coli) / References: UniProt: B6V311
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Ammonium sulfate,Sodium citrate tribasic dihydrate pH5.6, Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.27→35.19 Å / Num. obs: 32017 / % possible obs: 99.3 % / Redundancy: 6.6 % / CC1/2: 0.984 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.072 / Rrim(I) all: 0.185 / Χ2: 0.87 / Net I/σ(I): 8.9 / Num. measured all: 210831
Reflection shellResolution: 2.27→2.33 Å / % possible obs: 98.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 2.055 / Num. measured all: 15789 / Num. unique obs: 2339 / CC1/2: 0.445 / Rpim(I) all: 0.849 / Χ2: 0.75 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→33.63 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 1754 5.49 %
Rwork0.227 --
obs0.2293 31958 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→33.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4189 0 0 71 4260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144293
X-RAY DIFFRACTIONf_angle_d1.5465788
X-RAY DIFFRACTIONf_dihedral_angle_d8.169545
X-RAY DIFFRACTIONf_chiral_restr0.087611
X-RAY DIFFRACTIONf_plane_restr0.01734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.330.38741310.32372215X-RAY DIFFRACTION95
2.33-2.40.37151680.31632275X-RAY DIFFRACTION98
2.4-2.480.34761390.30192271X-RAY DIFFRACTION99
2.48-2.560.35091080.28582348X-RAY DIFFRACTION98
2.56-2.670.37931170.26772313X-RAY DIFFRACTION99
2.67-2.790.3141230.26832334X-RAY DIFFRACTION99
2.79-2.930.32821400.24692324X-RAY DIFFRACTION99
2.93-3.120.27451360.22962323X-RAY DIFFRACTION99
3.12-3.360.3021370.24112325X-RAY DIFFRACTION99
3.36-3.70.26621390.21242345X-RAY DIFFRACTION99
3.7-4.230.21921550.19432315X-RAY DIFFRACTION100
4.23-5.330.21791220.18192389X-RAY DIFFRACTION100
5.33-33.630.21961390.21182427X-RAY DIFFRACTION100

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