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- PDB-6gxx: Fab fragment of an antibody selective for alpha-1-antitrypsin in ... -

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Basic information

Entry
Database: PDB / ID: 6gxx
TitleFab fragment of an antibody selective for alpha-1-antitrypsin in the native conformation
Components
  • FAB 1D9 heavy chain
  • FAB 1D9 light chain
KeywordsPROTEIN BINDING / Antibody fragment / Antitrypsin binding / Diagnostic / Monoclonal / conformationally-selective
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsElliston, E.L.K. / Miranda, E. / Perez, J. / Lomas, D.A. / Irving, J.A.
Funding support United Kingdom, United States, 5items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N024842/1 United Kingdom
Wellcome TrustWellcome Trust 4-year PhD Interdisciplinary Programme in Structural, Computational and Chemical Biology United Kingdom
Other privateAlpha-1 Foundation project grant to James Irving United States
Other privateAlpha-1 Foundation pilot grant to Elena Miranda United States
Other governmentUCLH/NIHR Biomedical Research Centre United Kingdom
CitationJournal: To Be Published
Title: Characterisation of a monoclonal antibody conformationally-selective for native alpha-1-antitrypsin
Authors: Elliston, E.L.K. / Miranda, E. / Perez, J. / Irving, J.A. / Lomas, D.A.
History
DepositionJun 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
H: FAB 1D9 heavy chain
L: FAB 1D9 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0453
Polymers48,0202
Non-polymers241
Water10,521584
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-41 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.103, 85.257, 89.427
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11H-586-

HOH

21L-492-

HOH

31L-510-

HOH

41L-569-

HOH

51L-687-

HOH

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Components

#1: Antibody FAB 1D9 heavy chain


Mass: 24161.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma / Organ: Spleen / Variant: BALB/c
#2: Antibody FAB 1D9 light chain


Mass: 23859.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma / Organ: Spleen / Variant: BALB/c
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.21 % / Description: Tabular
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG 3350, 0.1M Hepes, 0.05M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 11, 2018
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.85→29.81 Å / Num. obs: 34148 / % possible obs: 94.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 19.06 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.039 / Rrim(I) all: 0.139 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.8911.7421160.9350.2270.78398.1
9.08-29.8110.531.93560.9990.020.06997.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDS20171218data reduction
Aimlessv0.6.2data scaling
PHASERv2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mf2

1mf2


Resolution: 1.85→27.08 Å / SU ML: 0.2351 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4849
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 1718 5.05 %Random
Rwork0.186 ---
obs0.1878 34004 94.75 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 19.96 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 1 584 3831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373389
X-RAY DIFFRACTIONf_angle_d0.63734649
X-RAY DIFFRACTIONf_chiral_restr0.046531
X-RAY DIFFRACTIONf_plane_restr0.0044593
X-RAY DIFFRACTIONf_dihedral_angle_d11.8671203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.910.3751540.30062737X-RAY DIFFRACTION98.17
1.91-1.970.3027850.23871758X-RAY DIFFRACTION63.31
1.97-2.040.24031590.20062798X-RAY DIFFRACTION100
2.04-2.120.26981590.19572784X-RAY DIFFRACTION100
2.12-2.220.23291590.19672799X-RAY DIFFRACTION99.7
2.22-2.330.27831110.24532226X-RAY DIFFRACTION78.63
2.33-2.480.24661510.19552811X-RAY DIFFRACTION100
2.48-2.670.25111530.19142821X-RAY DIFFRACTION99.97
2.67-2.940.21971370.18482869X-RAY DIFFRACTION100
2.94-3.360.2061460.16782870X-RAY DIFFRACTION100
3.36-4.240.16691470.16062779X-RAY DIFFRACTION96.19
4.24-27.090.1971570.16673034X-RAY DIFFRACTION100

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