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- PDB-8xig: The crystal structure of the AEP domain of MPXV E5 -

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Basic information

Entry
Database: PDB / ID: 8xig
TitleThe crystal structure of the AEP domain of MPXV E5
ComponentsUncoating factor OPG117
KeywordsREPLICATION / primase
Function / homology
Function and homology information


helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / host cell cytoplasm / hydrolase activity / ATP binding
Similarity search - Function
DNA primase/nucleoside triphosphatase, C-terminal / Poxvirus D5 protein-like / Bacteriophage/plasmid primase, P4, C-terminal / D5 N terminal like / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PYROPHOSPHATE / Uncoating factor OPG117
Similarity search - Component
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGan, J. / Zhang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2024
Title: Structural and functional insights into the helicase protein E5 of Mpox virus.
Authors: Gan, J. / Zhang, W.
History
DepositionDec 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncoating factor OPG117
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1674
Polymers25,9401
Non-polymers2273
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-24 kcal/mol
Surface area10850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.982, 54.816, 74.845
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 Uncoating factor OPG117


Mass: 25940.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG117, MPXVgp100 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A7H0DN89, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-PPV / PYROPHOSPHATE / Pyrophosphate


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.98 Å3/Da / Density % sol: 37.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Magnesium formate dihydrate, 15% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 26185 / % possible obs: 99.1 % / Redundancy: 10.2 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.036 / Rrim(I) all: 0.123 / Χ2: 0.967 / Net I/σ(I): 7.4 / Num. measured all: 266804
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.65-1.716.90.49123950.8970.9720.1820.5260.84791.9
1.71-1.788.30.45825590.9320.9820.1560.4850.85599
1.78-1.869.20.38326030.9650.9910.1250.4030.86100
1.86-1.969.40.32425950.9730.9930.1070.3420.903100
1.96-2.0810.30.23226170.9890.9970.0730.2440.968100
2.08-2.2411.10.18626100.9920.9980.0560.1940.99100
2.24-2.4611.10.15326440.9920.9980.0460.161.043100
2.46-2.8211.60.12626500.9930.9980.0370.1311.048100
2.82-3.55120.10126850.9950.9990.030.1051.057100
3.55-3011.60.09228270.9940.9980.0280.0960.96499.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→27.41 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 20.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2163 1142 4.86 %
Rwork0.1731 --
obs0.1752 23492 88.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→27.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 2 358 2141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.97
X-RAY DIFFRACTIONf_dihedral_angle_d6.919253
X-RAY DIFFRACTIONf_chiral_restr0.06290
X-RAY DIFFRACTIONf_plane_restr0.009321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.730.2449870.1991767X-RAY DIFFRACTION57
1.73-1.820.2829750.20192191X-RAY DIFFRACTION70
1.82-1.930.23241210.19412669X-RAY DIFFRACTION85
1.93-2.080.20431770.17193021X-RAY DIFFRACTION98
2.08-2.290.24261590.16883127X-RAY DIFFRACTION100
2.29-2.620.23071850.17763109X-RAY DIFFRACTION100
2.62-3.30.20221820.17653144X-RAY DIFFRACTION100
3.3-27.410.19811560.15913322X-RAY DIFFRACTION100

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