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

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Basic information

Entry
Database: PDB / ID: 9lim
TitleCrystal structure of the monkeypox virus N-tagged I7L protease in the P212121 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: 2.32 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: I7L
B: I7L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8675
Polymers98,5792
Non-polymers2883
Water3,585199
1
A: I7L
hetero molecules

B: I7L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8675
Polymers98,5792
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3590 Å2
ΔGint-67 kcal/mol
Surface area31320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.992, 113.502, 193.144
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 I7L


Mass: 49289.652 Da / Num. of mol.: 2
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 12.5% PEG 8000, 0.1 M sodium acetate (pH 5.0), and 0.2 M lithium sulfate.

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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: 2.32→97.86 Å / Num. obs: 42335 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.429 / Rpim(I) all: 0.133 / Rrim(I) all: 0.45 / Χ2: 0.97 / Net I/σ(I): 5.9 / Num. measured all: 468188
Reflection shellResolution: 2.32→2.44 Å / % possible obs: 100 % / Redundancy: 11.4 % / Rmerge(I) obs: 4.066 / Num. measured all: 68872 / Num. unique obs: 6068 / CC1/2: 0.342 / Rpim(I) all: 1.248 / Rrim(I) all: 4.256 / Χ2: 0.94 / Net I/σ(I) obs: 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: 2.32→97.86 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 2050 4.87 %
Rwork0.2174 --
obs0.2186 42132 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→97.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6036 0 15 199 6250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026199
X-RAY DIFFRACTIONf_angle_d0.4218374
X-RAY DIFFRACTIONf_dihedral_angle_d17.1882222
X-RAY DIFFRACTIONf_chiral_restr0.037931
X-RAY DIFFRACTIONf_plane_restr0.0021048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.370.35571360.31612637X-RAY DIFFRACTION99
2.37-2.430.33491200.30962574X-RAY DIFFRACTION99
2.43-2.490.35331290.2972621X-RAY DIFFRACTION100
2.5-2.570.31621350.28742627X-RAY DIFFRACTION100
2.57-2.650.29161310.27332639X-RAY DIFFRACTION100
2.65-2.750.30531400.25782632X-RAY DIFFRACTION100
2.75-2.860.26931240.252692X-RAY DIFFRACTION100
2.86-2.990.26741470.24492615X-RAY DIFFRACTION100
2.99-3.140.24961280.23792661X-RAY DIFFRACTION100
3.14-3.340.26691580.22272667X-RAY DIFFRACTION100
3.34-3.60.2421500.19892669X-RAY DIFFRACTION100
3.6-3.960.19821280.1822703X-RAY DIFFRACTION100
3.96-4.530.20191440.16512694X-RAY DIFFRACTION100
4.53-5.710.18231370.18562763X-RAY DIFFRACTION100
5.71-97.860.2221430.2022888X-RAY DIFFRACTION99

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