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- PDB-5hum: The crystal structure of neuraminidase from A/Sichuan/26221/2014 ... -

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Basic information

Entry
Database: PDB / ID: 5hum
TitleThe crystal structure of neuraminidase from A/Sichuan/26221/2014 influenza virus
Componentsneuraminidase
KeywordsVIRAL PROTEIN / neuraminidase / influenza virus / H5Nx
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 / membrane => GO:0016020 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding
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: 1.6 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 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,78516
Polymers172,8554
Non-polymers1,93012
Water30,7341706
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15450 Å2
ΔGint-89 kcal/mol
Surface area48010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.335, 76.277, 117.211
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
neuraminidase


Mass: 43213.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/chicken/Sichuan/NCJPL1/2014(H5N6))
Strain: A/chicken/Sichuan/NCJPL1/2014(H5N6) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0B4N5Z5*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1706 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.47 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.2M Sodium Acetate, 0.1M Tris:HCL pH 8.5, 16% (w/v) PEG 4000

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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: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 272309 / % possible obs: 99.9 % / Redundancy: 3.7 % / Net I/σ(I): 22

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.6→34.803 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 13841 5.09 %
Rwork0.1977 --
obs0.1988 271704 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→34.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12048 0 116 1706 13870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01812504
X-RAY DIFFRACTIONf_angle_d1.68116924
X-RAY DIFFRACTIONf_dihedral_angle_d12.4354552
X-RAY DIFFRACTIONf_chiral_restr0.0921824
X-RAY DIFFRACTIONf_plane_restr0.012192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.27084490.2388389X-RAY DIFFRACTION97
1.6182-1.63720.25934870.21368507X-RAY DIFFRACTION100
1.6372-1.65720.22864800.19238684X-RAY DIFFRACTION100
1.6572-1.67820.22944740.19298499X-RAY DIFFRACTION100
1.6782-1.70020.23594280.19368578X-RAY DIFFRACTION100
1.7002-1.72350.24284560.19498628X-RAY DIFFRACTION100
1.7235-1.74820.21734420.19228643X-RAY DIFFRACTION100
1.7482-1.77430.21414530.18978605X-RAY DIFFRACTION100
1.7743-1.8020.23694690.19198461X-RAY DIFFRACTION100
1.802-1.83150.22095150.18328585X-RAY DIFFRACTION100
1.8315-1.86310.21434560.18268631X-RAY DIFFRACTION100
1.8631-1.8970.22074520.18258524X-RAY DIFFRACTION100
1.897-1.93350.20924650.17648537X-RAY DIFFRACTION100
1.9335-1.97290.21914480.17898640X-RAY DIFFRACTION100
1.9729-2.01580.19594090.18518630X-RAY DIFFRACTION100
2.0158-2.06270.23164410.19188678X-RAY DIFFRACTION100
2.0627-2.11430.21644870.19858535X-RAY DIFFRACTION100
2.1143-2.17140.23784540.21058597X-RAY DIFFRACTION100
2.1714-2.23530.22464750.2068615X-RAY DIFFRACTION100
2.2353-2.30750.2165210.19258546X-RAY DIFFRACTION100
2.3075-2.38990.20414450.19288596X-RAY DIFFRACTION100
2.3899-2.48560.23544410.19528663X-RAY DIFFRACTION100
2.4856-2.59870.22394480.19358688X-RAY DIFFRACTION100
2.5987-2.73560.22273920.19718680X-RAY DIFFRACTION100
2.7356-2.90690.20914660.20998594X-RAY DIFFRACTION100
2.9069-3.13120.23514880.20588627X-RAY DIFFRACTION100
3.1312-3.44610.22054780.20878687X-RAY DIFFRACTION100
3.4461-3.94420.20694850.19938640X-RAY DIFFRACTION100
3.9442-4.96690.18864840.1758701X-RAY DIFFRACTION100
4.9669-34.81130.24764530.22988475X-RAY DIFFRACTION95

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