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- PDB-3cl2: N1 Neuraminidase N294S + Oseltamivir -

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Basic information

Entry
Database: PDB / ID: 3cl2
TitleN1 Neuraminidase N294S + Oseltamivir
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / HYDROLASE / N1 / Neuraminidase / N294S / Oseltamivir / Glycosidase / Membrane / Transmembrane / Virion
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / identical protein binding / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-G39 / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / Resolution: 2.538 Å
AuthorsCollins, P. / Haire, L.F. / Lin, Y.P. / Liu, J. / Russell, R.J. / Walker, P.A. / Skehel, J.J. / Martin, S.R. / Hay, A.J. / Gamblin, S.J.
CitationJournal: Nature / Year: 2008
Title: Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants.
Authors: Collins, P.J. / Haire, L.F. / Lin, Y.P. / Liu, J. / Russell, R.J. / Walker, P.A. / Skehel, J.J. / Martin, S.R. / Hay, A.J. / Gamblin, S.J.
History
DepositionMar 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 22, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / entity_src_nat / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _entity.src_method / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
E: Neuraminidase
F: Neuraminidase
G: Neuraminidase
H: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,53816
Polymers337,2638
Non-polymers2,2758
Water0
1
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,7698
Polymers168,6324
Non-polymers1,1374
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15090 Å2
ΔGint-54 kcal/mol
Surface area42230 Å2
MethodPISA
2
E: Neuraminidase
F: Neuraminidase
G: Neuraminidase
H: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,7698
Polymers168,6324
Non-polymers1,1374
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15200 Å2
ΔGint-54.8 kcal/mol
Surface area42090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)290.649, 290.649, 133.293
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein
Neuraminidase /


Mass: 42157.891 Da / Num. of mol.: 8 / Fragment: UNP residues 63-447 / Mutation: N294S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NA / Production host: Influenza A virus / Strain (production host): WSN-NA (H1N1) / References: UniProt: Q6DPL2, exo-alpha-sialidase
#2: Chemical
ChemComp-G39 / (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid / Oseltamivir carboxylate / Oseltamivir


Mass: 284.351 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H24N2O4 / Comment: medication, antivirus*YM

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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: 4.82 Å3/Da / Density % sol: 74.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 15% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.54→29.8 Å / Num. obs: 190670 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.7 Å / % possible all: 88.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.538→29.853 Å / FOM work R set: 0.837 / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 9563 5.02 %
Rwork0.239 --
obs0.24 190670 90.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 13.87 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 0.41 Å2 / Biso mean: 17.05 Å2 / Biso min: 125.13 Å2
Baniso -1Baniso -2Baniso -3
1--6.855 Å2-0 Å2-0 Å2
2---6.855 Å20 Å2
3----5.446 Å2
Refinement stepCycle: LAST / Resolution: 2.538→29.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23680 0 160 0 23840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924568
X-RAY DIFFRACTIONf_angle_d1.27633320
X-RAY DIFFRACTIONf_chiral_restr0.0893496
X-RAY DIFFRACTIONf_plane_restr0.0074312
X-RAY DIFFRACTIONf_dihedral_angle_d18.458664
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.538-2.5670.3392240.3014518474268
2.567-2.5970.312810.35777605887
2.597-2.6290.3223150.2995692600786
2.629-2.6620.3223340.295714604886
2.662-2.6970.3423050.2825704600987
2.697-2.7340.313300.2755738606886
2.734-2.7730.3093180.2795730604886
2.773-2.8150.3132960.2745766606287
2.815-2.8590.2953310.2635738606986
2.859-2.9050.3063010.2785682598385
2.905-2.9550.2893170.2715693601086
2.955-3.0090.32900.2695721601186
3.009-3.0670.3132670.2765684595185
3.067-3.1290.2952940.2755753604786
3.129-3.1970.2882780.2655655593385
3.197-3.2720.2922490.2555710595985
3.272-3.3530.2782850.2525613589884
3.353-3.4440.2622930.2395584587784
3.444-3.5450.2673150.2286184649992
3.545-3.6590.2443700.23266076977100
3.659-3.790.2443460.2236650699699
3.79-3.9410.233500.2116680703099
3.941-4.120.2253300.1926622695299
4.12-4.3370.1953570.18266937050100
4.337-4.6080.1893530.17166787031100
4.608-4.9620.1873660.16466607026100
4.962-5.4590.1843660.17966677033100
5.459-6.2420.2163650.19266967061100
6.242-7.8410.2243600.1936730709099
7.841-29.8550.2323770.2266768714599

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