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- PDB-8xif: The crystal structure of the AEP domain of VACV D5 -

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Basic information

Entry
Database: PDB / ID: 8xif
TitleThe crystal structure of the AEP domain of VACV D5
ComponentsUncoating factor OPG117
KeywordsREPLICATION / primase / VACV
Function / homology
Function and homology information


DNA primase activity / viral DNA genome replication / DNA replication, synthesis of primer / ribonucleoside triphosphate phosphatase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / host cell cytoplasm / 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 speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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)26,1814
Polymers25,9541
Non-polymers2273
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-26 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.470, 56.620, 74.160
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: 25954.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Gene: OPG117, VACWR110, D5R / Production host: Escherichia coli (E. coli)
References: UniProt: P04305, 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.: 172 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
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: BL10U2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.39→28.31 Å / Num. obs: 45138 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.029 / Rrim(I) all: 0.102 / Net I/σ(I): 13.8
Reflection shellResolution: 1.39→1.42 Å / Redundancy: 13 % / Rmerge(I) obs: 0.098 / Num. unique obs: 45138 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→28.31 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1972 2283 5.06 %
Rwork0.1791 --
obs0.18 45138 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→28.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 11 172 1986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081853
X-RAY DIFFRACTIONf_angle_d1.0482517
X-RAY DIFFRACTIONf_dihedral_angle_d6.779253
X-RAY DIFFRACTIONf_chiral_restr0.09292
X-RAY DIFFRACTIONf_plane_restr0.012326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.37441580.34572639X-RAY DIFFRACTION100
1.42-1.450.34741340.29912663X-RAY DIFFRACTION100
1.45-1.490.27781570.2642625X-RAY DIFFRACTION100
1.49-1.530.25461230.23422649X-RAY DIFFRACTION100
1.53-1.570.22091460.20342645X-RAY DIFFRACTION100
1.57-1.630.24831350.1912638X-RAY DIFFRACTION100
1.63-1.680.19651330.18472651X-RAY DIFFRACTION100
1.68-1.750.18161610.17872649X-RAY DIFFRACTION100
1.75-1.830.20181270.17742677X-RAY DIFFRACTION100
1.83-1.930.21611570.17962633X-RAY DIFFRACTION100
1.93-2.050.20521360.17132696X-RAY DIFFRACTION100
2.05-2.210.2011370.16972686X-RAY DIFFRACTION100
2.21-2.430.20271410.17962688X-RAY DIFFRACTION100
2.43-2.780.20611430.1842709X-RAY DIFFRACTION100
2.78-3.50.2131360.17412769X-RAY DIFFRACTION100
3.5-28.310.15331590.15752838X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 13.4521 Å / Origin y: 8.5366 Å / Origin z: 15.8979 Å
111213212223313233
T0.1385 Å20.0143 Å2-0.0083 Å2-0.1478 Å20.0144 Å2--0.1565 Å2
L0.8748 °20.2597 °2-0.144 °2-0.9475 °20.2643 °2--1.6586 °2
S-0.0059 Å °0.0062 Å °0.0359 Å °0.0015 Å °0.0547 Å °0.0128 Å °0.0166 Å °-0.0034 Å °-0.0489 Å °
Refinement TLS groupSelection details: all

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