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- PDB-6pzd: Crystal structure of the neuraminidase stabilization mutant Y169a... -

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Basic information

Entry
Database: PDB / ID: 6pzd
TitleCrystal structure of the neuraminidase stabilization mutant Y169aH from A/Shanghai/2/2013 (H7N9)
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / antibody / inhibition mechanism
Function / homology
Function and homology information


exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / exo-alpha-(2->3)-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / integral component of membrane / metal ion binding
Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily / Sialidase, Influenza viruses A/B / Neuraminidase - #10 / 6 Propeller / Neuraminidase / Mainly Beta
Neuraminidase / Neuraminidase / polysac:dmanpa1-2dmanpa1-2dmanpa1-3[dmanpa1-2dmanpa1-3[dmanpa1-6]dmanpa1-6]dmanpb1-4dglcpnacb1-4dglcpnacb1-:
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsZhu, X. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400024C United States
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _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

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Assembly

Deposited unit
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,50210
Polymers44,0141
Non-polymers2,4889
Water10,683593
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,01040
Polymers176,0564
Non-polymers9,95436
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation23_555-z,y,x1
Unit cell
γ
α
β
Length a, b, c (Å)182.219, 182.219, 182.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-886-

HOH

21A-1060-

HOH

31A-1181-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuraminidase /


Mass: 44014.000 Da / Num. of mol.: 1 / Mutation: Y169H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Shanghai/02/2013(H7N9))
Strain: A/Shanghai/02/2013(H7N9) / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: V9NZ28, UniProt: R4NFR6*PLUS, exo-alpha-sialidase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 4 types, 600 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Chemical ChemComp-CA / CALCIUM ION / Calcium


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 12% PEG20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.12→43 Å / Num. obs: 194141 / % possible obs: 99.9 % / Redundancy: 22.3 % / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rsym value: 0.1 / Net I/σ(I): 30.8
Reflection shellResolution: 1.12→1.13 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6246 / CC1/2: 0.834 / Rpim(I) all: 0.45 / Rsym value: 0.92

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L14

5l14


Resolution: 1.12→42.949 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 9.57
RfactorNum. reflection% reflection
Rfree0.128 9726 5.01 %
Rwork0.1122 --
Obs0.113 194104 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.12→42.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3064 0 163 593 3820
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083572
X-RAY DIFFRACTIONf_angle_d1.1714942
X-RAY DIFFRACTIONf_dihedral_angle_d14.851431
X-RAY DIFFRACTIONf_chiral_restr0.091557
X-RAY DIFFRACTIONf_plane_restr0.009623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
1.1198-1.13260.24493100.26415905X-RAY DIFFRACTION97
1.1326-1.14590.26883180.22816067X-RAY DIFFRACTION99
1.1459-1.15990.21112980.18796100X-RAY DIFFRACTION100
1.1599-1.17450.17713550.16256057X-RAY DIFFRACTION100
1.1745-1.190.15763080.15216122X-RAY DIFFRACTION100
1.19-1.20630.1543400.13686046X-RAY DIFFRACTION100
1.2063-1.22350.14183000.1286169X-RAY DIFFRACTION100
1.2235-1.24180.14733450.11986040X-RAY DIFFRACTION100
1.2418-1.26120.1473480.11716060X-RAY DIFFRACTION100
1.2612-1.28190.13322980.11926143X-RAY DIFFRACTION100
1.2819-1.3040.13143250.10396095X-RAY DIFFRACTION100
1.304-1.32770.12283370.10366101X-RAY DIFFRACTION100
1.3277-1.35320.10843140.09536120X-RAY DIFFRACTION100
1.3532-1.38090.11073200.09136141X-RAY DIFFRACTION100
1.3809-1.41090.10853340.0876094X-RAY DIFFRACTION100
1.4109-1.44370.09743300.08626081X-RAY DIFFRACTION100
1.4437-1.47980.112960.08326168X-RAY DIFFRACTION100
1.4798-1.51980.10223160.08286150X-RAY DIFFRACTION100
1.5198-1.56450.10463290.0846124X-RAY DIFFRACTION100
1.5645-1.61510.09983390.08386135X-RAY DIFFRACTION100
1.6151-1.67280.10943530.08446108X-RAY DIFFRACTION100
1.6728-1.73980.11213170.08956164X-RAY DIFFRACTION100
1.7398-1.81890.11173120.09446185X-RAY DIFFRACTION100
1.8189-1.91480.10823030.16194X-RAY DIFFRACTION100
1.9148-2.03480.11293490.10196165X-RAY DIFFRACTION100
2.0348-2.19190.1293020.10136255X-RAY DIFFRACTION100
2.1919-2.41250.11153250.10366216X-RAY DIFFRACTION100
2.4125-2.76150.12263410.11176246X-RAY DIFFRACTION100
2.7615-3.4790.12333460.11596317X-RAY DIFFRACTION100
3.479-42.9810.15723180.13736610X-RAY DIFFRACTION100

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