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

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Basic information

Entry
Database: PDB / ID: 7fge
TitleA naturally-occurring neuraminidase-inhibitors-resistant NA from asiatic toad influenza B-like virus
Componentstoad NA (PER)
KeywordsVIRAL PROTEIN / neuraminidase
Function / homologyChem-BCZ
Function and homology information
Biological speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.1Aug 10, 2022Group: Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Nov 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 1.3Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: toad NA (PER)
B: toad NA (PER)
C: toad NA (PER)
D: toad NA (PER)
E: toad NA (PER)
F: toad NA (PER)
G: toad NA (PER)
H: toad NA (PER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)431,61824
Polymers428,6708
Non-polymers2,94816
Water3,279182
1
A: toad NA (PER)
B: toad NA (PER)
E: toad NA (PER)
F: toad NA (PER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,80912
Polymers214,3354
Non-polymers1,4748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: toad NA (PER)
D: toad NA (PER)
G: toad NA (PER)
H: toad NA (PER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,80912
Polymers214,3354
Non-polymers1,4748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.215, 135.124, 135.449
Angle α, β, γ (deg.)90.000, 103.850, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"

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
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH

NCS oper:
IDCodeMatrixVector
1given(0.94293215465, 0.242182912369, 0.228530935943), (-0.234609271, -0.00384098826472, 0.972082165648), (0.236299474582, -0.970223007234, 0.0531965651791)5.14083687439, -18.8165837093, -21.0257101184
2given(0.969836212741, 0.214640627472, 0.115529742899), (-0.215319337398, 0.532194998364, 0.818783284306), (0.114259806574, -0.818961467198, 0.562358259339)-3.66633205884, 59.6734209123, 50.5353540687
3given(0.892788469138, 0.127585041079, 0.43203102512), (-0.129454831526, -0.845935365033, 0.517334325925), (0.431474444166, -0.517798624447, -0.73872483954)-4.89086723766, 31.2454801224, 54.6705311389
4given(0.888341766154, 0.0147438616135, 0.458946102555), (0.0151241476829, -0.999881569841, 0.0028471827611), (0.458933727964, 0.00441189727096, -0.888459548038)0.922609928551, -40.6599894113, -2.61471873536
5given(0.943135270625, -0.230844966833, 0.239178725205), (0.246694639632, 0.00381955264732, -0.969085737071), (0.222795009099, 0.972983048314, 0.0605505707235)-4.37822841214, -21.7799698127, 18.34927704
6given(0.914784913162, -0.199876196951, 0.351024313322), (0.198553638545, -0.534275546906, -0.821660570187), (0.351774096931, 0.821339847975, -0.449061063618)-11.6761996071, 35.44317485, 82.1736733041
7given(0.993038332206, -0.112857198799, 0.0337360852666), (0.113829588011, 0.845778805508, -0.521249495967), (0.0302934920907, 0.521460894825, 0.85273726288)-10.4700387376, 63.8645304032, 78.1189420282

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Components

#1: Protein
toad NA (PER)


Mass: 53583.793 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / Production host: Baculovirus expression vector pFastBac1-HM
#2: Chemical
ChemComp-BCZ / 3-(1-ACETYLAMINO-2-ETHYL-BUTYL)-4-GUANIDINO-2-HYDROXY-CYCLOPENTANECARBOXYLIC ACID / BCX-1812


Mass: 328.407 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H28N4O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: antivirus, inhibitor*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
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: 0.9792 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: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 125177 / % possible obs: 95.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 38.51 Å2 / CC1/2: 0.986 / Rpim(I) all: 0.084 / Net I/σ(I): 12.9
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 11423 / CC1/2: 0.706 / Rpim(I) all: 0.578

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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: 2.8→46.03 Å / SU ML: 0.4297 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.2673
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2909 1988 2.27 %
Rwork0.2303 85667 -
obs0.2317 87655 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.84 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23368 0 192 182 23742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010423968
X-RAY DIFFRACTIONf_angle_d1.489332480
X-RAY DIFFRACTIONf_chiral_restr0.06853728
X-RAY DIFFRACTIONf_plane_restr0.01864192
X-RAY DIFFRACTIONf_dihedral_angle_d8.49993352
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.711740023683
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.820920113559
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.794913500199
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.727772390217
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.726216604785
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.821401493463
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.821941361746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.45081370.32465945X-RAY DIFFRACTION94.22
2.87-2.950.38341370.31525925X-RAY DIFFRACTION94.07
2.95-3.030.38431380.30585927X-RAY DIFFRACTION94.25
3.03-3.130.33421370.28935938X-RAY DIFFRACTION94.27
3.13-3.240.39621390.27875959X-RAY DIFFRACTION94.57
3.24-3.370.31991410.25266031X-RAY DIFFRACTION95.87
3.37-3.530.32111400.25746079X-RAY DIFFRACTION96.7
3.53-3.710.381420.30826075X-RAY DIFFRACTION96.46
3.71-3.950.27241420.22976178X-RAY DIFFRACTION97.65
3.95-4.250.29781460.2036285X-RAY DIFFRACTION99
4.25-4.680.19841460.16476295X-RAY DIFFRACTION99.66
4.68-5.350.21161470.16726322X-RAY DIFFRACTION99.92
5.35-6.740.25091480.19596366X-RAY DIFFRACTION99.91
6.74-46.030.21511480.18446342X-RAY DIFFRACTION98.23
Refinement TLS params.Method: refined / Origin x: 16.9786874085 Å / Origin y: 13.5483161203 Å / Origin z: 37.4755329491 Å
111213212223313233
T0.833713080313 Å20.00959391898704 Å20.191113677484 Å2-0.204120563174 Å20.0364238287591 Å2--0.257130543212 Å2
L0.0109246150789 °20.0254253372161 °2-0.0331381076276 °2-0.0663344430084 °20.0575060186683 °2--0.125415285096 °2
S-0.0158012131453 Å °-0.0180102508672 Å °0.0213596319165 Å °-0.0925465669251 Å °0.00526109120252 Å °0.0192028262854 Å °0.00616922076787 Å °0.00235449404944 Å °-0.0058200243046 Å °
Refinement TLS groupSelection details: all

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