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- PDB-9lik: Crystal structure of the C-tagged I7L protease from monkeypox virus -

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Basic information

Entry
Database: PDB / ID: 9lik
TitleCrystal structure of the C-tagged I7L protease from monkeypox virus
ComponentsI7L
KeywordsVIRAL PROTEIN / cysteine protease
Function / homologyPeptidase C57, Vaccinia virus protein I7 / Vaccinia virus I7 processing peptidase / cysteine-type peptidase activity / Papain-like cysteine peptidase superfamily / virion component / proteolysis / I7L
Function and homology information
Biological speciesMonkeypox virus Zaire-96-I-16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsYou, M.Y. / Wang, Y.H. / Su, H.X. / Li, M.J. / Xu, Y.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Adv Sci / Year: 2025
Title: Dynamic Cap-Mediated Substrate Access and Potent Inhibitor Design of Monkeypox Virus I7L Protease.
Authors: Su, H. / Wu, G. / Xiong, M. / Wang, Y. / Cao, J. / You, M. / Xiang, Y. / Nie, T. / Li, M. / Xiao, G. / Zhang, L. / Shao, Q. / Xu, Y.
History
DepositionJan 14, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: I7L
A: I7L


Theoretical massNumber of molelcules
Total (without water)99,7672
Polymers99,7672
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-31 kcal/mol
Surface area35210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.158, 187.158, 69.509
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein I7L


Mass: 49883.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus Zaire-96-I-16 / Gene: I7L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8V512
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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: 3.52 Å3/Da / Density % sol: 65.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 5-20% PEG 4000, 0.15 M imidazole-MES buffer (pH 5.5-6.5), 30% glycerol, and 0.6 M halogen salts (NaF: NaBr: NaI = 1: 1: 1)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.64→162.08 Å / Num. obs: 41167 / % possible obs: 100 % / Redundancy: 20.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.029 / Rrim(I) all: 0.132 / Χ2: 0.91 / Net I/σ(I): 19.1 / Num. measured all: 830846
Reflection shellResolution: 2.64→2.71 Å / % possible obs: 100 % / Redundancy: 20.3 % / Rmerge(I) obs: 2.558 / Num. measured all: 61293 / Num. unique obs: 3013 / CC1/2: 0.731 / Rpim(I) all: 0.579 / Rrim(I) all: 2.623 / Χ2: 0.93 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→44.95 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2701 2053 5.02 %
Rwork0.2424 --
obs0.2438 40932 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.64→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6351 0 0 10 6361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066498
X-RAY DIFFRACTIONf_angle_d0.958800
X-RAY DIFFRACTIONf_dihedral_angle_d8.942869
X-RAY DIFFRACTIONf_chiral_restr0.056991
X-RAY DIFFRACTIONf_plane_restr0.0081117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.70.37771220.33532586X-RAY DIFFRACTION99
2.7-2.770.32491330.31672582X-RAY DIFFRACTION100
2.77-2.840.31511140.31652574X-RAY DIFFRACTION99
2.84-2.930.36061060.30972589X-RAY DIFFRACTION99
2.93-3.020.40421920.31692545X-RAY DIFFRACTION99
3.02-3.130.37741500.29362529X-RAY DIFFRACTION99
3.13-3.250.32571160.27572583X-RAY DIFFRACTION100
3.26-3.40.28871370.26732613X-RAY DIFFRACTION100
3.4-3.580.30421370.2612571X-RAY DIFFRACTION100
3.58-3.810.2551500.24692597X-RAY DIFFRACTION100
3.81-4.10.26521230.2322627X-RAY DIFFRACTION100
4.1-4.510.24131440.20492588X-RAY DIFFRACTION100
4.51-5.170.22411440.20932622X-RAY DIFFRACTION100
5.17-6.50.23111610.24612615X-RAY DIFFRACTION100
6.51-44.950.26051240.21172658X-RAY DIFFRACTION98

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