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- PDB-9lil: Crystal structure of the monkeypox virus N-tagged I7L protease in... -

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Basic information

Entry
Database: PDB / ID: 9lil
TitleCrystal structure of the monkeypox virus N-tagged I7L protease in the I4 space group
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsWang, 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

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Assembly

Deposited unit
A: I7L


Theoretical massNumber of molelcules
Total (without water)49,2901
Polymers49,2901
Non-polymers00
Water2,018112
1
A: I7L

A: I7L


Theoretical massNumber of molelcules
Total (without water)98,5792
Polymers98,5792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3350 Å2
ΔGint-38 kcal/mol
Surface area33060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.912, 94.912, 114.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein I7L


Mass: 49289.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus (strain 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.: 112 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 15% PEG3350, 0.1 M Bis-Tris (pH 5.5), and 0.2 M potassium thiocyanate.

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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: Oct 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.21→72.97 Å / Num. obs: 25443 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.319 / Rpim(I) all: 0.094 / Rrim(I) all: 0.332 / Χ2: 0.93 / Net I/σ(I): 7.2 / Num. measured all: 313052
Reflection shellResolution: 2.21→2.32 Å / % possible obs: 100 % / Redundancy: 12.4 % / Rmerge(I) obs: 4.399 / Num. measured all: 46188 / Num. unique obs: 3711 / CC1/2: 0.397 / Rpim(I) all: 1.292 / Rrim(I) all: 4.587 / Χ2: 0.93 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→67.11 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 1218 4.8 %
Rwork0.1978 --
obs0.1996 25354 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→67.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 0 112 3219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033180
X-RAY DIFFRACTIONf_angle_d0.584289
X-RAY DIFFRACTIONf_dihedral_angle_d15.0781151
X-RAY DIFFRACTIONf_chiral_restr0.041475
X-RAY DIFFRACTIONf_plane_restr0.003537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.290.3131350.31092614X-RAY DIFFRACTION98
2.29-2.40.30611420.26952667X-RAY DIFFRACTION99
2.4-2.520.29751580.25352656X-RAY DIFFRACTION100
2.52-2.680.32991280.23682683X-RAY DIFFRACTION100
2.68-2.890.3731100.23852700X-RAY DIFFRACTION100
2.89-3.180.25021320.2222682X-RAY DIFFRACTION100
3.18-3.640.22261440.19632704X-RAY DIFFRACTION100
3.64-4.580.18121310.15592705X-RAY DIFFRACTION100
4.59-67.110.19141380.16342725X-RAY DIFFRACTION99

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