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- PDB-7wn7: Crystal structure of HearNPV P26 -

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Basic information

Entry
Database: PDB / ID: 7wn7
TitleCrystal structure of HearNPV P26
Componentsp26
KeywordsHYDROLASE / nuclease
Function / homologyNucleopolyhedrovirus p26 protein / Poxin, virus / 2',3'-cyclic GMP-AMP binding / nuclease activity / p26
Function and homology information
Biological speciesHelicoverpa armigera nucleopolyhedrovirus G4
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKuang, W. / Hu, Z. / Gong, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170156 China
CitationJournal: Nat Commun / Year: 2022
Title: Dual roles and evolutionary implications of P26/poxin in antagonizing intracellular cGAS-STING and extracellular melanization immunity.
Authors: Yin, M. / Kuang, W. / Wang, Q. / Wang, X. / Yuan, C. / Lin, Z. / Zhang, H. / Deng, F. / Jiang, H. / Gong, P. / Zou, Z. / Hu, Z. / Wang, M.
History
DepositionJan 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: p26
B: p26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4248
Polymers68,0292
Non-polymers3956
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-59 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.749, 69.236, 52.746
Angle α, β, γ (deg.)90.000, 102.180, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein p26


Mass: 34014.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicoverpa armigera nucleopolyhedrovirus G4
Plasmid: pET32 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99H25
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 6.7 / Details: PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 52908 / % possible obs: 97.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 24.72 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.035 / Rrim(I) all: 0.081 / Χ2: 0.57 / Net I/σ(I): 5.1 / Num. measured all: 253451
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.974.60.33951140.9520.1570.3750.50294.7
1.97-2.054.60.26851770.9690.1280.2990.50195.3
2.05-2.144.80.2252030.9750.1040.2440.52996.3
2.14-2.2550.1752700.9880.0780.1880.55497.1
2.25-2.394.90.13853200.9910.0640.1530.55197.3
2.39-2.584.70.1152390.9920.0530.1230.58896.8
2.58-2.8450.09153240.9950.0410.10.60897.8
2.84-3.254.80.07153820.9960.0330.0780.67498.2
3.25-4.094.90.05353940.9970.0250.0590.6298.5
4.09-304.70.04654850.9960.0230.0520.55698.4

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→28.74 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 2562 5 %
Rwork0.1836 48707 -
obs0.1849 51269 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.89 Å2 / Biso mean: 31.6194 Å2 / Biso min: 15.49 Å2
Refinement stepCycle: final / Resolution: 1.9→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3907 0 18 296 4221
Biso mean--37.47 36.26 -
Num. residues----493
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.940.33031490.26732596274592
1.94-1.980.26031370.23652680281793
1.98-2.020.2351410.22332621276293
2.02-2.070.25971350.21552632276792
2.07-2.120.26531260.20382737286395
2.12-2.170.25651250.20332715284095
2.17-2.240.24431290.19172729285895
2.24-2.310.21811250.18642722284795
2.31-2.390.22811260.19832702282895
2.39-2.490.23491300.19332641277193
2.49-2.60.21841610.19232690285195
2.6-2.740.24091520.1982740289296
2.74-2.910.25151410.20292726286796
2.91-3.140.21581880.19652710289896
3.14-3.450.2131780.17642707288595
3.45-3.950.17061570.15782745290296
3.95-4.970.14071350.14862752288795
4.97-28.740.20641270.17512862298996

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