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- PDB-5z88: Crystal structure of H5 hemagglutinin G228S mutant with 3SLN from... -

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Basic information

Entry
Database: PDB / ID: 5z88
TitleCrystal structure of H5 hemagglutinin G228S mutant with 3SLN from A/chicken/Taiwan/0502/2012
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / influenza virus / H5N2
Function / homologyHemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Alpha-Beta Complex / Alpha Beta
Function and homology information
Biological speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLin, T.H. / Lee, M.S. / Wu, W.G. / Liu, J.S.
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. / Liu, J.S.
History
DepositionJan 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_unobs_or_zero_occ_atoms / refine_hist / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _refine_hist.d_res_high / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)66,8322
Polymers66,3611
Non-polymers4711
Water00
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,4966
Polymers199,0823
Non-polymers1,4143
Water0
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 area14480 Å2
ΔGint-38 kcal/mol
Surface area62290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.227, 110.227, 314.193
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: 66360.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / Production host: Baculoviridae (virus)
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.56 %
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: Aug 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 13555 / % possible obs: 98.6 % / Redundancy: 3.5 % / CC1/2: 0.966 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.049 / Rrim(I) all: 0.094 / Net I/σ(I): 13.3
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.506 / CC1/2: 0.87 / Rpim(I) all: 0.324 / Rrim(I) all: 0.605 / Rsym value: 0.301

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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: 5YT9

5yt9


Resolution: 3→28.121 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.98
RfactorNum. reflection% reflection
Rfree0.2927 650 4.8 %
Rwork0.2136 --
obs0.2174 13545 88.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→28.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3939 0 31 0 3970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014064
X-RAY DIFFRACTIONf_angle_d1.1945498
X-RAY DIFFRACTIONf_dihedral_angle_d8.692423
X-RAY DIFFRACTIONf_chiral_restr0.06587
X-RAY DIFFRACTIONf_plane_restr0.006713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9853-3.21550.2841860.27141586X-RAY DIFFRACTION56
3.2155-3.53850.40231300.25712543X-RAY DIFFRACTION88
3.5385-4.04930.29871420.21172831X-RAY DIFFRACTION98
4.0493-5.09670.24541480.18632892X-RAY DIFFRACTION99
5.0967-28.12240.28851440.20863043X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 119.5715 Å / Origin y: -14.8024 Å / Origin z: 60.8909 Å
111213212223313233
T0.3656 Å20.013 Å2-0.0263 Å2-0.19 Å20.0612 Å2--0.3067 Å2
L0.8947 °2-0.2678 °20.121 °2-1.1317 °20.7626 °2--2.5391 °2
S-0.0418 Å °-0.2145 Å °-0.0509 Å °0.4085 Å °0.1666 Å °-0.12 Å °0.5247 Å °0.1145 Å °-0.0777 Å °
Refinement TLS groupSelection details: all

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