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- PDB-6ntf: Crystal structure of a computationally optimized H5 influenza hem... -

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Basic information

Entry
Database: PDB / ID: 6ntf
TitleCrystal structure of a computationally optimized H5 influenza hemagglutinin
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / vaccine / influenza
Function / homologyHemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Alpha-Beta Complex / Alpha Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHuang, J. / Bar-Peled, Y. / Mousa, J.J.
CitationJournal: Vaccine / Year: 2019
Title: Structural and antigenic characterization of a computationally-optimized H5 hemagglutinin influenza vaccine.
Authors: Bar-Peled, Y. / Huang, J. / Nunez, I.A. / Pierce, S.R. / Ecker, J.W. / Ross, T.M. / Mousa, J.J.
History
DepositionJan 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 / struct_asym / struct_conn / struct_conn_type / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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)65,60814
Polymers63,5741
Non-polymers2,03413
Water0
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,82542
Polymers190,7223
Non-polymers6,10239
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area20310 Å2
ΔGint-20 kcal/mol
Surface area63530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.518, 101.518, 450.084
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: 63574.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / Production host: Homo sapiens (human)
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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.: 3
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: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 3.88 Å3/Da / Density % sol: 68.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 400, 200 mM MgCl2.6H2O, and 100 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→48.082 Å / Num. obs: 22588 / % possible obs: 99.1 % / Redundancy: 11.1 % / Biso Wilson estimate: 79.19 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1277 / Rpim(I) all: 0.04025 / Rrim(I) all: 0.1341 / Net I/σ(I): 14.73
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3148 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 2212 / CC1/2: 0.966 / Rpim(I) all: 0.3148 / Rrim(I) all: 0.4451 / % possible all: 98.78

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2fk0

2fk0


Resolution: 2.8→48.082 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.88
RfactorNum. reflection% reflection
Rfree0.275 1093 4.87 %
Rwork0.2366 --
obs0.2386 22428 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 0 0 4056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084151
X-RAY DIFFRACTIONf_angle_d1.3335623
X-RAY DIFFRACTIONf_dihedral_angle_d35.7431496
X-RAY DIFFRACTIONf_chiral_restr0.077612
X-RAY DIFFRACTIONf_plane_restr0.006729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.92750.48721390.4152592X-RAY DIFFRACTION99
2.9275-3.08180.39211380.36562612X-RAY DIFFRACTION98
3.0818-3.27490.37781090.31492640X-RAY DIFFRACTION98
3.2749-3.52770.33361530.28482595X-RAY DIFFRACTION99
3.5277-3.88250.28841390.24252642X-RAY DIFFRACTION99
3.8825-4.4440.24781240.21372695X-RAY DIFFRACTION100
4.444-5.59760.25441470.2042718X-RAY DIFFRACTION100
5.5976-48.08870.22211440.20482841X-RAY DIFFRACTION100

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