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- PDB-5hun: The crystal structure of neuraminidase from A/gyrfalcon/Washingto... -

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Basic information

Entry
Database: PDB / ID: 5hun
TitleThe crystal structure of neuraminidase from A/gyrfalcon/Washington/41088-6/2014 influenza virus
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / neuraminidase / influenza virus / H5Nx
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsYang, H. / Carney, P.J. / Guo, Z. / Chang, J.C. / Stevens, J.
CitationJournal: J.Virol. / Year: 2016
Title: Molecular Characterizations of Surface Proteins Hemagglutinin and Neuraminidase from Recent H5Nx Avian Influenza Viruses.
Authors: Yang, H. / Carney, P.J. / Mishin, V.P. / Guo, Z. / Chang, J.C. / Wentworth, D.E. / Gubareva, L.V. / Stevens, J.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0002
Polymers43,9601
Non-polymers401
Water1,67593
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,0018
Polymers175,8414
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_865-x+3,-y+1,z1
crystal symmetry operation3_745-y+2,x-1,z1
crystal symmetry operation4_675y+1,-x+2,z1
Buried area13940 Å2
ΔGint-125 kcal/mol
Surface area45770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.652, 90.652, 110.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Neuraminidase


Mass: 43960.281 Da / Num. of mol.: 1 / Fragment: unp residues 80-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/gyrfalcon/Washington/41088-6/2014(H5N8))
Strain: A/gyrfalcon/Washington/41088-6/2014(H5N8) / Gene: NA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0C4WVM3, exo-alpha-sialidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.16 M Calcium Acetate, 0.08 M Sodium Cacodylate:HCl pH 6.5, 14.4% (w/v) PEG 8000, 20% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 19878 / % possible obs: 99.8 % / Redundancy: 6.3 % / Net I/σ(I): 47.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.114 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23704 1006 5.1 %RANDOM
Rwork0.20066 ---
obs0.20262 18882 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.382 Å2
Baniso -1Baniso -2Baniso -3
1--4.13 Å20 Å20 Å2
2---4.13 Å20 Å2
3---8.26 Å2
Refinement stepCycle: 1 / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 1 93 3110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193100
X-RAY DIFFRACTIONr_bond_other_d0.0030.022818
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9254214
X-RAY DIFFRACTIONr_angle_other_deg0.81236480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.615388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75623.099142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53515487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.111526
X-RAY DIFFRACTIONr_chiral_restr0.0890.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213571
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02759
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8212.9011555
X-RAY DIFFRACTIONr_mcbond_other1.8222.9011554
X-RAY DIFFRACTIONr_mcangle_it2.734.3461942
X-RAY DIFFRACTIONr_mcangle_other2.734.3461943
X-RAY DIFFRACTIONr_scbond_it2.3123.1391545
X-RAY DIFFRACTIONr_scbond_other2.3133.1391543
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5394.622272
X-RAY DIFFRACTIONr_long_range_B_refined5.07523.853533
X-RAY DIFFRACTIONr_long_range_B_other5.05623.783517
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 66 -
Rwork0.207 1401 -
obs--99.93 %
Refinement TLS params.Method: refined / Origin x: 113.9413 Å / Origin y: 28.5607 Å / Origin z: -123.3539 Å
111213212223313233
T0.0136 Å2-0.0205 Å2-0.0065 Å2-0.0331 Å2-0.0051 Å2--0.1719 Å2
L0.6062 °20.0023 °2-0.0631 °2-0.5879 °2-0.0516 °2--0.0397 °2
S-0.0015 Å °0.0001 Å °-0.1332 Å °-0.0071 Å °0.0021 Å °0.1881 Å °-0.0186 Å °0.0304 Å °-0.0005 Å °

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