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- PDB-6kcj: Crystal structure of H5N2 hemagglutinin Apo-Q226L mutant from A/c... -

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Basic information

Entry
Database: PDB / ID: 6kcj
TitleCrystal structure of H5N2 hemagglutinin Apo-Q226L mutant from A/chicken/Taiwan/0502/2012
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / influenza virus / H5N2
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsLin, T.H. / Lee, M.S. / Wu, W.G.
CitationJournal: To Be Published
Title: crystal structure of H5 hemagglutinin from A/chicken/Taiwan/0502/2012
Authors: Lin, T.H. / Lee, M.S. / Wu, W.G.
History
DepositionJun 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5372
Polymers66,3161
Non-polymers2211
Water2,036113
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,6106
Polymers198,9473
Non-polymers6643
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Buried area13440 Å2
ΔGint-28 kcal/mol
Surface area63020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.439, 110.439, 314.139
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Hemagglutinin /


Mass: 66315.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/chicken/Taiwan/0502/2012(H5N2))
Strain: A/chicken/Taiwan/0502/2012(H5N2) / Gene: HA / Production host: unidentified baculovirus / References: UniProt: A0A059VBQ9
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris, 0.2M MgCl, 16%PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.46→30 Å / Num. obs: 27258 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.042 / Rrim(I) all: 0.14 / Net I/σ(I): 21.4
Reflection shellResolution: 2.46→2.55 Å / Rmerge(I) obs: 1.415 / Mean I/σ(I) obs: 2 / Num. unique obs: 2682 / CC1/2: 0.83 / Rpim(I) all: 0.441 / Rrim(I) all: 1.483 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YKC

5ykc


Resolution: 2.46→28.152 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.25
RfactorNum. reflection% reflection
Rfree0.2593 1327 5.28 %
Rwork0.2031 --
obs0.206 25125 92.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.46→28.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3953 0 14 113 4080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084060
X-RAY DIFFRACTIONf_angle_d1.0495494
X-RAY DIFFRACTIONf_dihedral_angle_d9.7332424
X-RAY DIFFRACTIONf_chiral_restr0.057586
X-RAY DIFFRACTIONf_plane_restr0.005715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4601-2.55860.3352890.2791521X-RAY DIFFRACTION54
2.5586-2.67490.33851150.26952154X-RAY DIFFRACTION76
2.6749-2.81590.35321500.26222801X-RAY DIFFRACTION99
2.8159-2.99210.32561610.25632864X-RAY DIFFRACTION100
2.9921-3.22280.30891830.22862806X-RAY DIFFRACTION100
3.2228-3.54660.29711280.21132884X-RAY DIFFRACTION100
3.5466-4.05850.23831650.17782870X-RAY DIFFRACTION100
4.0585-5.10820.17791490.15572906X-RAY DIFFRACTION100
5.1082-28.15390.2361870.19412992X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 119.7962 Å / Origin y: -14.8325 Å / Origin z: 60.9848 Å
111213212223313233
T0.2664 Å20.0315 Å2-0.0223 Å2-0.1394 Å20.0325 Å2--0.2337 Å2
L0.626 °2-0.0857 °20.0585 °2-0.6094 °20.2465 °2--0.5868 °2
S-0.0171 Å °-0.1067 Å °-0.0149 Å °0.1985 Å °0.13 Å °-0.0992 Å °0.2626 Å °0.0547 Å °-0.0321 Å °
Refinement TLS groupSelection details: all

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