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- PDB-5y2k: A human antibody AF4H1L1 -

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Basic information

Entry
Database: PDB / ID: 5y2k
TitleA human antibody AF4H1L1
Components
  • a group 2 HA binding antibody AF4H1K1 Fab heavy chain
  • a group 2 HA binding antibody AF4H1K1 Fab light chain
KeywordsIMMUNE SYSTEM / influenza virus / H3-clade / neutralizing antibody / H7N9-infected patient / next generation sequencing
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXiao, H. / Qi, J. / Gao, F.G.
CitationJournal: To Be Published
Title: An H3-clade neutralizing antibody screened from an H7N9 patient that binds group 2 influenza A hemagglutinins
Authors: Xiao, H. / Qi, J. / Gao, F.G.
History
DepositionJul 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
Revision 1.2Nov 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: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
B: a group 2 HA binding antibody AF4H1K1 Fab light chain
C: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
D: a group 2 HA binding antibody AF4H1K1 Fab light chain
E: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
F: a group 2 HA binding antibody AF4H1K1 Fab light chain
G: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
H: a group 2 HA binding antibody AF4H1K1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)193,5798
Polymers193,5798
Non-polymers00
Water10,178565
1
A: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
B: a group 2 HA binding antibody AF4H1K1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,3952
Polymers48,3952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-28 kcal/mol
Surface area19860 Å2
MethodPISA
2
C: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
D: a group 2 HA binding antibody AF4H1K1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,3952
Polymers48,3952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-27 kcal/mol
Surface area19470 Å2
MethodPISA
3
E: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
F: a group 2 HA binding antibody AF4H1K1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,3952
Polymers48,3952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-28 kcal/mol
Surface area19620 Å2
MethodPISA
4
G: a group 2 HA binding antibody AF4H1K1 Fab heavy chain
H: a group 2 HA binding antibody AF4H1K1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,3952
Polymers48,3952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-26 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.266, 90.119, 111.404
Angle α, β, γ (deg.)90.00, 102.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
a group 2 HA binding antibody AF4H1K1 Fab heavy chain


Mass: 24977.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293T / Production host: Homo sapiens (human)
#2: Antibody
a group 2 HA binding antibody AF4H1K1 Fab light chain


Mass: 23417.818 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293T / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Bicine pH9.0, 2% v/v 1,4-Dioxane, 10% w/v PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 118899 / % possible obs: 98 % / Redundancy: 6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 25.1
Reflection shellResolution: 2.1→2.8 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 11093 / % possible all: 92.3

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Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PY8

4py8


Resolution: 2.1→41.63 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.259 5966 -
Rwork0.22 --
obs-118836 98 %
Refinement stepCycle: LAST / Resolution: 2.1→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12898 0 0 565 13463

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