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

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Basic information

Entry
Database: PDB / ID: 7fgd
TitleA naturally-occurring neuraminidase-inhibitors-resistant NA from asiatic toad influenza B-like virus
Componentstoad NA (OSE)
KeywordsVIRAL PROTEIN / neuraminidase
Function / homologyChem-G39
Function and homology information
Biological speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Oct 30, 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 (OSE)
B: toad NA (OSE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8166
Polymers107,1682
Non-polymers6494
Water11,944663
1
A: toad NA (OSE)
B: toad NA (OSE)
hetero molecules

A: toad NA (OSE)
B: toad NA (OSE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,63312
Polymers214,3354
Non-polymers1,2988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area14880 Å2
ΔGint-99 kcal/mol
Surface area45020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.991, 142.275, 120.556
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
Components on special symmetry positions
IDModelComponents
11B-868-

HOH

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: (-0.000244111562515, -0.0075643481082, 0.999971360113), (-0.000186416839343, 0.999971372877, 0.00756430269694), (-0.999999952829, -0.000184564966635, -0.00024551469617) ...NCS oper: (Code: given
Matrix: (-0.000244111562515, -0.0075643481082, 0.999971360113), (-0.000186416839343, 0.999971372877, 0.00756430269694), (-0.999999952829, -0.000184564966635, -0.00024551469617)
Vector: 29.9612144405, -0.182301696911, 90.1622508608)

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Components

#1: Protein toad NA (OSE)


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-G39 / (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid / Oseltamivir carboxylate


Mass: 284.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H24N2O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / 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: 2.4 Å3/Da / Density % sol: 48.76 %
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 PILATUS3 S 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: 2.1→50 Å / Num. obs: 60226 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 35.8 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.031 / Net I/σ(I): 11.7
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 5980 / CC1/2: 0.772 / Rpim(I) all: 0.389

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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: 2.1→18.35 Å / SU ML: 0.241 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2531
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245 1995 3.41 %
Rwork0.204 56578 -
obs0.2054 58573 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→18.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5842 0 42 663 6547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00825986
X-RAY DIFFRACTIONf_angle_d0.98758110
X-RAY DIFFRACTIONf_chiral_restr0.0575930
X-RAY DIFFRACTIONf_plane_restr0.00621046
X-RAY DIFFRACTIONf_dihedral_angle_d6.6729838
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.408508224935 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.30531200.26413373X-RAY DIFFRACTION81.54
2.15-2.210.30971320.26483757X-RAY DIFFRACTION91.68
2.21-2.280.2941390.25873943X-RAY DIFFRACTION95.6
2.28-2.350.30921400.25433964X-RAY DIFFRACTION97.16
2.35-2.430.31191440.25824086X-RAY DIFFRACTION98.97
2.43-2.530.2611450.2454119X-RAY DIFFRACTION99.46
2.53-2.640.28231450.23264104X-RAY DIFFRACTION99.39
2.64-2.780.28781440.22744101X-RAY DIFFRACTION99.11
2.78-2.960.24681460.21624111X-RAY DIFFRACTION99.7
2.96-3.180.26031460.20024155X-RAY DIFFRACTION99.56
3.18-3.50.24631470.18644140X-RAY DIFFRACTION99.74
3.5-4.010.18951480.16754204X-RAY DIFFRACTION99.91
4.01-5.030.1851480.15344186X-RAY DIFFRACTION99.59
5.03-18.350.24031510.19914335X-RAY DIFFRACTION99.53
Refinement TLS params.Method: refined / Origin x: 78.5181247455 Å / Origin y: 20.1939961068 Å / Origin z: 22.7059816648 Å
111213212223313233
T0.160097914138 Å2-0.0173712873287 Å20.00828148343806 Å2-0.188239382511 Å2-0.00651408420583 Å2--0.210881445978 Å2
L0.321484901631 °20.0320032744074 °20.107208598992 °2-0.192950524127 °20.0016312796168 °2--0.751706179651 °2
S-0.00459659086165 Å °0.0255583361275 Å °0.0198380937213 Å °-0.0155346332272 Å °0.00854086167032 Å °-0.0510607362831 Å °-0.0259704058356 Å °0.17955411125 Å °-0.0017738489058 Å °
Refinement TLS groupSelection details: all

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