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- PDB-8ixw: Tilapia lake virus S8 segment -

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Basic information

Entry
Database: PDB / ID: 8ixw
TitleTilapia lake virus S8 segment
ComponentsChains: A,B
KeywordsVIRUS / Tilapia lake virus / S8 segment
Function / homologyselenourea / Nucleocapsid protein
Function and homology information
Biological speciesTilapia lake virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsWang, Z.X. / Zhang, Y.A. / Ouyang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725026, 82225028, 82172287 China
CitationJournal: To Be Published
Title: Structure and function of tilapia lake virus S8 segment
Authors: Wang, Z.X. / Zhang, Y.A.
History
DepositionApr 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 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: Chains: A,B
B: Chains: A,B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8038
Polymers39,0652
Non-polymers7386
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-40 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.486, 51.342, 52.706
Angle α, β, γ (deg.)106.865, 108.918, 108.022
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Chains: A,B


Mass: 19532.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tilapia lake virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y9SHR5
#2: Chemical
ChemComp-SEY / selenourea


Mass: 123.016 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH4N2Se / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion
Details: 0.08 M Potassium chloride, 0.02 M Barium chloride dihydrate, 0.04 M Sodium cacodylate trihydrate pH 6.0, 40% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride.

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Data collection

DiffractionMean temperature: 298.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→20.96 Å / Num. obs: 38281 / % possible obs: 96.24 % / Redundancy: 3.6 % / Biso Wilson estimate: 26.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.03903 / Rpim(I) all: 0.02444 / Rrim(I) all: 0.0462 / Net I/σ(I): 20.12
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.2111 / Num. unique obs: 3781 / CC1/2: 0.982 / Rpim(I) all: 0.1272 / Rrim(I) all: 0.2468

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.19.2_4158phasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→20.96 Å / SU ML: 0.1786 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 19.0587
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2032 1905 4.98 %
Rwork0.1765 36357 -
obs0.1776 38262 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.15 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 24 303 2924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00432643
X-RAY DIFFRACTIONf_angle_d0.86523549
X-RAY DIFFRACTIONf_chiral_restr0.0442427
X-RAY DIFFRACTIONf_plane_restr0.0063453
X-RAY DIFFRACTIONf_dihedral_angle_d4.8226355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.30211600.22872511X-RAY DIFFRACTION94.75
1.85-1.890.26792000.21372510X-RAY DIFFRACTION95.73
1.89-1.950.20031470.2182601X-RAY DIFFRACTION96.15
1.95-2.010.22181310.21632591X-RAY DIFFRACTION96.52
2.01-2.090.25231330.19892588X-RAY DIFFRACTION96.35
2.09-2.170.19831550.19492588X-RAY DIFFRACTION96.48
2.17-2.270.22811780.18612564X-RAY DIFFRACTION96.48
2.27-2.390.1991850.18672582X-RAY DIFFRACTION96.21
2.39-2.540.18261250.18562589X-RAY DIFFRACTION96.79
2.54-2.730.20961250.17932624X-RAY DIFFRACTION96.52
2.73-3.010.19651540.17242600X-RAY DIFFRACTION97.01
3.01-3.440.2432400.17632713X-RAY DIFFRACTION96.77
3.44-4.330.16491050.15662641X-RAY DIFFRACTION97.07
4.33-20.960.1866670.16042655X-RAY DIFFRACTION95.68

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