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- PDB-7fgb: A naturally-occurring neuraminidase-inhibitors-resistant NA from ... -

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Basic information

Entry
Database: PDB / ID: 7fgb
TitleA naturally-occurring neuraminidase-inhibitors-resistant NA from asiatic toad influenza B-like virus
Componentstoad NA
KeywordsVIRAL PROTEIN / neuraminidase / asiatic toad
Biological speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChai, Y. / Wu, Y. / Gao, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31872745 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structural and inhibitor sensitivity analysis of influenza B-like viral neuraminidases derived from Asiatic toad and spiny eel.
Authors: Li, L. / Chai, Y. / Peng, W. / Li, D. / Sun, L. / Gao, G.F. / Qi, J. / Xiao, H. / Liu, W.J. / von Itzstein, M. / Gao, F.
History
DepositionJul 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: toad NA
B: toad NA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8828
Polymers107,1682
Non-polymers7156
Water13,403744
1
A: toad NA
B: toad NA
hetero molecules

A: toad NA
B: toad NA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,76516
Polymers214,3354
Non-polymers1,42912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area13360 Å2
ΔGint-139 kcal/mol
Surface area46720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.446, 143.150, 120.284
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 80 - 466 / Label seq-ID: 103 - 489

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (0.00140729764689, -0.00353606134936, -0.999992757866), (-0.000219034686906, 0.999993723025, -0.00353637301148), (0.999998985768, 0.000224009830044, 0.00140651429323) ...NCS oper: (Code: given
Matrix: (0.00140729764689, -0.00353606134936, -0.999992757866), (-0.000219034686906, 0.999993723025, -0.00353637301148), (0.999998985768, 0.000224009830044, 0.00140651429323)
Vector: 30.0571845964, 0.0785444380065, 30.0576843204)

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Components

#1: Protein toad NA


Mass: 53583.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / Production host: Baculovirus expression vector pFastBac1-HM
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 744 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate monohydrate, 0.1 M sodium citrate tribasic dihydrate pH 5.0, 26% v/v polyethylene 200.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 70237 / % possible obs: 98.7 % / Redundancy: 11.6 % / Biso Wilson estimate: 34.9 Å2 / CC1/2: 0.992 / Rpim(I) all: 5.6 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 6890 / CC1/2: 0.834 / Rpim(I) all: 31.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B9S

1b9s


Resolution: 2→18.64 Å / SU ML: 0.2806 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7534
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2725 3518 5.1 %
Rwork0.2293 65414 -
obs0.2315 68932 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.8 Å2
Refinement stepCycle: LAST / Resolution: 2→18.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5842 0 40 744 6626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085982
X-RAY DIFFRACTIONf_angle_d1.12488106
X-RAY DIFFRACTIONf_chiral_restr0.0573932
X-RAY DIFFRACTIONf_plane_restr0.00681044
X-RAY DIFFRACTIONf_dihedral_angle_d6.7366846
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.449509003859 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.30691500.30372461X-RAY DIFFRACTION93.72
2.03-2.060.30111420.28832488X-RAY DIFFRACTION95.05
2.06-2.090.34831430.29522517X-RAY DIFFRACTION94.8
2.09-2.120.31261610.28952524X-RAY DIFFRACTION97.18
2.12-2.150.31871320.28312555X-RAY DIFFRACTION97.32
2.15-2.190.37221320.30152597X-RAY DIFFRACTION97.71
2.19-2.230.30541450.27992582X-RAY DIFFRACTION97.78
2.23-2.270.31811390.27962605X-RAY DIFFRACTION98.07
2.27-2.320.32861190.26632579X-RAY DIFFRACTION98.14
2.32-2.370.30431420.2682638X-RAY DIFFRACTION98.65
2.37-2.430.34741390.27482606X-RAY DIFFRACTION98.78
2.43-2.490.35791450.27572605X-RAY DIFFRACTION98.96
2.49-2.550.3421260.26682623X-RAY DIFFRACTION98.42
2.55-2.630.2941410.26252625X-RAY DIFFRACTION98.86
2.63-2.710.31671220.26122643X-RAY DIFFRACTION98.96
2.71-2.810.3491320.25142633X-RAY DIFFRACTION98.61
2.81-2.920.32461360.24852669X-RAY DIFFRACTION99.5
2.92-3.050.30611530.23722620X-RAY DIFFRACTION99.18
3.05-3.210.26761460.22012647X-RAY DIFFRACTION99.36
3.21-3.410.29331510.21212648X-RAY DIFFRACTION99.43
3.41-3.680.24371660.19462626X-RAY DIFFRACTION99.22
3.68-4.040.20851510.17372683X-RAY DIFFRACTION99.75
4.04-4.620.16371530.15842699X-RAY DIFFRACTION99.44
4.62-5.790.18721170.1742724X-RAY DIFFRACTION99.65
5.79-18.640.25971350.24012817X-RAY DIFFRACTION99.13
Refinement TLS params.Method: refined / Origin x: -18.5812073168 Å / Origin y: -20.4096746012 Å / Origin z: 22.4487216517 Å
111213212223313233
T0.149656747939 Å2-0.0105558130604 Å2-0.00583298439893 Å2-0.179166735815 Å20.0125002181734 Å2--0.178418805438 Å2
L0.198806652639 °2-0.00881595803346 °2-0.117110103114 °2-0.126591241125 °2-0.00802738273654 °2--0.539864795777 °2
S0.00337853160017 Å °-0.00630958214527 Å °-0.0095891534873 Å °-0.00370434036063 Å °0.00852211608208 Å °0.035414902748 Å °0.0111776414606 Å °-0.0722589977991 Å °-0.00803454619524 Å °
Refinement TLS groupSelection details: all

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