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- PDB-6z2t: Three-dimensional structure of an influenza hemagglutinin LAH pro... -

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Basic information

Entry
Database: PDB / ID: 6z2t
TitleThree-dimensional structure of an influenza hemagglutinin LAH protein in its post-fusion conformation
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / Hemagglutinin stem / Long alpha helix / Influenza / Post-fusion conformation / Tri-stalk protein
Function / homologyHaemagglutinin, influenzavirus B / Haemagglutinin / Haemagglutinin, influenzavirus A/B / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / membrane / PHOSPHATE ION / Hemagglutinin
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsKirsteina, A. / Kazaks, A. / Tars, K.
CitationJournal: To Be Published
Title: Three-dimensional structure of an influenza hemagglutinin LAH protein
Authors: Kirsteina, A. / Kazaks, A. / Tars, K.
History
DepositionMay 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)7,0602
Polymers6,9651
Non-polymers951
Water84747
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1796
Polymers20,8943
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area5100 Å2
ΔGint-41 kcal/mol
Surface area10610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.780, 36.780, 166.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-101-

PO4

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Components

#1: Protein Hemagglutinin


Mass: 6964.825 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Mexico City/63/2009(H1N1))
Production host: Escherichia coli (E. coli) / References: UniProt: C6KNC6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 0.15 M H6NO4P and 40% MPD; pH 6.7; protein 10 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2017 / Details: RH-COATED TOROIDAL SI MIRROR
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.34→55.52 Å / Num. obs: 15916 / % possible obs: 99.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 20.069 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.3
Reflection shellResolution: 1.34→1.42 Å / Redundancy: 7 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2234 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GOL

6gol


Resolution: 1.34→41.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.479 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 766 4.8 %RANDOM
Rwork0.2154 ---
obs0.2165 15072 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.34 Å2 / Biso mean: 25.219 Å2 / Biso min: 15.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20.51 Å20 Å2
2--1.01 Å2-0 Å2
3----3.28 Å2
Refinement stepCycle: final / Resolution: 1.34→41.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms484 0 5 47 536
Biso mean--27.04 33.43 -
Num. residues----57
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.013494
X-RAY DIFFRACTIONr_bond_other_d0.0180.017456
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.639665
X-RAY DIFFRACTIONr_angle_other_deg1.7311.5971061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.767556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72124.37532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9281599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.772153
X-RAY DIFFRACTIONr_chiral_restr0.0850.260
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02537
X-RAY DIFFRACTIONr_gen_planes_other0.0090.0296
LS refinement shellResolution: 1.343→1.378 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 58 -
Rwork0.389 1065 -
all-1123 -
obs--98.16 %

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