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

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Basic information

Entry
Database: PDB / ID: 7fgc
TitleA naturally-occurring neuraminidase-inhibitors-resistant NA from asiatic toad influenza B-like virus
Componentstoad NA (ZMR)
KeywordsVIRAL PROTEIN / neuraminidase / toad / crystal strucuture
Function / homologyZANAMIVIR
Function and homology information
Biological speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: toad NA (ZMR)
B: toad NA (ZMR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9126
Polymers107,1682
Non-polymers7454
Water15,961886
1
A: toad NA (ZMR)
B: toad NA (ZMR)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)215,82512
Polymers214,3354
Non-polymers1,4908
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area14760 Å2
ΔGint-76 kcal/mol
Surface area45800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.232, 143.029, 120.082
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: (0.00226787354801, -0.00449947077944, 0.999987305676), (0.00120840774007, 0.999989159488, 0.00449673856998), (-0.999996698245, 0.0011981943657, 0.00227328615841)Vector: ...NCS oper: (Code: given
Matrix: (0.00226787354801, -0.00449947077944, 0.999987305676), (0.00120840774007, 0.999989159488, 0.00449673856998), (-0.999996698245, 0.0011981943657, 0.00227328615841)
Vector: 29.9518179871, -0.192046821534, 90.0903298324)

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Components

#1: Protein toad NA (ZMR)


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: Sugar ChemComp-ZMR / ZANAMIVIR / 4-GUANIDINO-2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / 4-guanidino-Neu5Ac2en / MODIFIED SIALIC ACID


Type: D-saccharide / Mass: 332.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N4O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*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.: 886 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
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: 1.89→50 Å / Num. obs: 80931 / % possible obs: 99.8 % / Redundancy: 12.7 % / Biso Wilson estimate: 30.8 Å2 / CC1/2: 0.995 / Rsym value: 0.065 / Net I/σ(I): 14.3
Reflection shellResolution: 1.89→1.96 Å / Mean I/σ(I) obs: 8.9 / Num. unique obs: 7894 / CC1/2: 0.881 / Rpim(I) all: 0.281

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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: 1.9→18.76 Å / SU ML: 0.2335 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2506
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2464 4041 5.02 %
Rwork0.2119 76451 -
obs0.2137 80492 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.53 Å2
Refinement stepCycle: LAST / Resolution: 1.9→18.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5842 0 48 886 6776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00755992
X-RAY DIFFRACTIONf_angle_d1.00558120
X-RAY DIFFRACTIONf_chiral_restr0.0583934
X-RAY DIFFRACTIONf_plane_restr0.00671048
X-RAY DIFFRACTIONf_dihedral_angle_d6.7611834
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.385100255772 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.35421050.30162050X-RAY DIFFRACTION78.19
1.92-1.950.34481480.29822585X-RAY DIFFRACTION97.64
1.95-1.970.3141340.27712602X-RAY DIFFRACTION98.84
1.97-20.32981260.27282630X-RAY DIFFRACTION99.24
2-2.020.30251400.25972646X-RAY DIFFRACTION99.43
2.02-2.050.30431510.25132591X-RAY DIFFRACTION99.42
2.05-2.080.28561360.24932650X-RAY DIFFRACTION99.79
2.08-2.120.32781400.24162653X-RAY DIFFRACTION100
2.12-2.150.26381350.23972628X-RAY DIFFRACTION99.89
2.15-2.190.29721420.24432632X-RAY DIFFRACTION99.75
2.19-2.230.26061560.23242631X-RAY DIFFRACTION99.57
2.23-2.270.28781390.23582650X-RAY DIFFRACTION99.82
2.27-2.320.24721350.22212614X-RAY DIFFRACTION99.82
2.32-2.370.271500.22942666X-RAY DIFFRACTION99.93
2.37-2.420.29241400.22812638X-RAY DIFFRACTION99.68
2.42-2.480.32711240.23012661X-RAY DIFFRACTION99.93
2.48-2.550.28241450.23172649X-RAY DIFFRACTION99.86
2.55-2.620.26131440.22342656X-RAY DIFFRACTION99.86
2.62-2.710.25921330.23112654X-RAY DIFFRACTION99.89
2.71-2.80.24361420.21012663X-RAY DIFFRACTION99.82
2.8-2.920.28121490.21372669X-RAY DIFFRACTION99.93
2.92-3.050.28731370.20422661X-RAY DIFFRACTION99.93
3.05-3.210.23441530.20062660X-RAY DIFFRACTION99.93
3.21-3.410.21981360.19132676X-RAY DIFFRACTION99.79
3.41-3.670.22371370.18582672X-RAY DIFFRACTION99.65
3.67-4.040.19881280.17912719X-RAY DIFFRACTION99.89
4.04-4.610.17351500.16582710X-RAY DIFFRACTION99.79
4.61-5.780.20431520.18082696X-RAY DIFFRACTION99.75
5.78-18.760.20361340.21592839X-RAY DIFFRACTION99.6
Refinement TLS params.Method: refined / Origin x: 78.6516911532 Å / Origin y: 20.1644493349 Å / Origin z: 22.4368122181 Å
111213212223313233
T0.155813416173 Å2-0.00520678904418 Å20.00709118107536 Å2-0.170144496957 Å2-0.00704613876979 Å2--0.185886900148 Å2
L0.184462956612 °20.0187665824141 °20.106229646381 °2-0.139663248488 °20.00611356846168 °2--0.496534355824 °2
S-0.00310556216946 Å °0.00256713856454 Å °0.00792315280198 Å °0.00345767992154 Å °0.0125198750138 Å °-0.0219638209593 Å °-0.0248597936259 Å °0.0615088171478 Å °-0.00801427756037 Å °
Refinement TLS groupSelection details: all

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