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- PDB-8wqk: Crystal structure of the C-terminal domain of PEDV nucleocapsid p... -

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Basic information

Entry
Database: PDB / ID: 8wqk
TitleCrystal structure of the C-terminal domain of PEDV nucleocapsid protein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / PEDV / Nucleocapsid protein
Function / homology
Function and homology information


viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / ribonucleoprotein complex / RNA binding
Similarity search - Function
Nucleocapsid protein, alphacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile.
Similarity search - Domain/homology
Biological speciesPorcine epidemic diarrhea virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.88 Å
AuthorsZhang, J.T. / Jiao, Z. / Liang, R. / Shi, Y.J. / Peng, G.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of the C-terminal domain of PEDV nucleocapsid protein
Authors: Zhang, J.T. / Jiao, Z. / Liang, R. / Shi, Y.J. / Peng, G.Q.
History
DepositionOct 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
F: Nucleoprotein
G: Nucleoprotein
H: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)101,6268
Polymers101,6268
Non-polymers00
Water1,71195
1
A: Nucleoprotein
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)25,4072
Polymers25,4072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-32 kcal/mol
Surface area9850 Å2
MethodPISA
2
B: Nucleoprotein
G: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)25,4072
Polymers25,4072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-39 kcal/mol
Surface area9810 Å2
MethodPISA
3
C: Nucleoprotein
E: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)25,4072
Polymers25,4072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-35 kcal/mol
Surface area9540 Å2
MethodPISA
4
F: Nucleoprotein
H: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)25,4072
Polymers25,4072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-41 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.920, 93.502, 97.200
Angle α, β, γ (deg.)90.00, 97.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nucleoprotein


Mass: 12703.262 Da / Num. of mol.: 8 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine epidemic diarrhea virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q07499
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium Chloride 0.1 M Bis-Tris:HCl pH 6.5 25% (w/v) PEG 3350

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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 PILATUS 2M / Detector: PIXEL / Date: Oct 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.52→67.12 Å / Num. obs: 25960 / % possible obs: 81.3 % / Redundancy: 5.1 % / CC1/2: 0.962 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.071 / Rrim(I) all: 0.172 / Χ2: 0.94 / Net I/σ(I): 6.1 / Num. measured all: 131448
Reflection shellResolution: 2.52→2.65 Å / % possible obs: 46.3 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.83 / Num. measured all: 5161 / Num. unique obs: 2139 / CC1/2: 0.453 / Rpim(I) all: 0.678 / Rrim(I) all: 1.081 / Χ2: 0.56 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
autoPROCdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.88→26.24 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2753 1049 5.22 %
Rwork0.2203 --
obs0.2232 20089 94.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.88→26.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6097 0 0 95 6192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0286227
X-RAY DIFFRACTIONf_angle_d1.8878434
X-RAY DIFFRACTIONf_dihedral_angle_d18.8792248
X-RAY DIFFRACTIONf_chiral_restr0.085909
X-RAY DIFFRACTIONf_plane_restr0.021120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-3.030.42341440.31112608X-RAY DIFFRACTION91
3.03-3.220.33791850.26392850X-RAY DIFFRACTION100
3.22-3.470.3081340.25262542X-RAY DIFFRACTION88
3.47-3.820.31311400.24472585X-RAY DIFFRACTION90
3.82-4.370.26641290.19352617X-RAY DIFFRACTION90
4.37-5.490.21091560.18512905X-RAY DIFFRACTION100
5.5-100.22871610.19972933X-RAY DIFFRACTION99

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