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- PDB-9ku9: Structure of mpox core protease mutant -

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Basic information

Entry
Database: PDB / ID: 9ku9
TitleStructure of mpox core protease mutant
ComponentsMPXVgp068
KeywordsVIRAL PROTEIN / orthopoxvirus / mpox / 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 / MPXVgp068
Function and homology information
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsDong, X. / Wang, H. / Ji, X. / Gao, Y. / Wang, W. / Yang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81902063 China
CitationJournal: To Be Published
Title: Structure of mpox core protease mutant
Authors: Dong, X. / Wang, H. / Ji, X. / Gao, Y. / Wang, W. / Yang, H.
History
DepositionDec 3, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: MPXVgp068
C: MPXVgp068


Theoretical massNumber of molelcules
Total (without water)98,8062
Polymers98,8062
Non-polymers00
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-33 kcal/mol
Surface area32050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.734, 113.500, 192.813
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 MPXVgp068 / Viral core cysteine proteinase


Mass: 49402.785 Da / Num. of mol.: 2 / Mutation: I215K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus
Gene: MPXV-USA2003_099_GR-066, MPXV-USA2003_206_DM-066, MPXV-USA2003_223_RS-066, MPXV_USA2003_039_073, MPXV_USA2003_044_073
Production host: Escherichia coli (E. coli) / References: UniProt: Q3I7P9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium sulfate, 20% w/v polyethylene glycol (PEG) 3350, pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.199→42.54 Å / Num. obs: 91758 / % possible obs: 99.9 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.097 / Net I/σ(I): 17.44
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.2-2.331.01477150.6411.1111
2.33-2.490.71173120.8750.7621
2.49-2.690.42968370.9590.4551
2.69-2.950.27262740.9880.2861
2.95-3.290.14957620.9960.1561
3.29-3.80.07850750.9980.0821
3.8-4.640.0543560.9990.0531
4.64-6.530.04734260.9990.051
6.53-42.540.03520510.9990.0371

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.199→42.54 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 3759 4.1 %
Rwork0.188 --
obs0.1895 91699 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.199→42.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6021 0 0 251 6272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066167
X-RAY DIFFRACTIONf_angle_d0.7468302
X-RAY DIFFRACTIONf_dihedral_angle_d14.1613675
X-RAY DIFFRACTIONf_chiral_restr0.047907
X-RAY DIFFRACTIONf_plane_restr0.0051034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.199-2.22640.34151350.32273091X-RAY DIFFRACTION94
2.2264-2.25570.34141380.29813226X-RAY DIFFRACTION97
2.2557-2.28660.29221340.29373171X-RAY DIFFRACTION99
2.2866-2.31930.32831370.2683223X-RAY DIFFRACTION100
2.3193-2.35390.311440.25763299X-RAY DIFFRACTION100
2.3539-2.39070.33011380.25533296X-RAY DIFFRACTION100
2.3907-2.42990.27391380.24383228X-RAY DIFFRACTION100
2.4299-2.47180.27061360.23293321X-RAY DIFFRACTION100
2.4718-2.51670.29441470.22613294X-RAY DIFFRACTION100
2.5167-2.56510.26431350.2183196X-RAY DIFFRACTION100
2.5651-2.61740.24031450.20063273X-RAY DIFFRACTION100
2.6174-2.67440.21021450.1873336X-RAY DIFFRACTION100
2.6744-2.73660.22431340.19243211X-RAY DIFFRACTION100
2.7366-2.8050.27111410.1953292X-RAY DIFFRACTION100
2.805-2.88080.2211370.18953288X-RAY DIFFRACTION100
2.8808-2.96560.23261400.18643259X-RAY DIFFRACTION100
2.9656-3.06120.1991430.18433335X-RAY DIFFRACTION100
3.0612-3.17060.20581330.18663203X-RAY DIFFRACTION100
3.1706-3.29750.25781400.18563346X-RAY DIFFRACTION100
3.2975-3.44750.20281350.18083204X-RAY DIFFRACTION100
3.4475-3.62920.20561410.17143296X-RAY DIFFRACTION100
3.6292-3.85640.22871400.16953291X-RAY DIFFRACTION100
3.8564-4.1540.23011410.16323228X-RAY DIFFRACTION100
4.154-4.57160.16591370.1463278X-RAY DIFFRACTION100
4.5716-5.23210.18221400.15883286X-RAY DIFFRACTION100
5.2321-6.58790.22481420.20583261X-RAY DIFFRACTION100
6.5879-42.540.19721430.1883208X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -9.6342 Å / Origin y: -6.2534 Å / Origin z: -40.4007 Å
111213212223313233
T0.275 Å20.0008 Å2-0.0086 Å2-0.2726 Å20.0243 Å2--0.3077 Å2
L0.849 °20.1482 °2-0.7195 °2-0.1175 °2-0.1673 °2--1.0556 °2
S0.0021 Å °-0.076 Å °-0.0842 Å °0.0426 Å °0.0041 Å °-0.0014 Å °-0.1039 Å °0.0417 Å °-0.0181 Å °
Refinement TLS groupSelection details: all

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