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- PDB-6i1o: Fab fragment of an antibody selective for wild-type alpha-1-antit... -

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Basic information

Entry
Database: PDB / ID: 6i1o
TitleFab fragment of an antibody selective for wild-type alpha-1-antitrypsin
Components
  • FAB 2H2 heavy chain
  • FAB 2H2 light chain
KeywordsPROTEIN BINDING / Antibody fragment / Antitrypsin binding / Diagnostic / Monoclonal / selective / wild-type / Glu342 / E342
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLaffranchi, M. / Elliston, E.L.K. / Miranda, E. / Perez, J. / Fra, A. / Lomas, D.A. / Irving, J.A.
Funding support United Kingdom, Italy, United States, 4items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N024842/1 United Kingdom
Other privateFondazione Cariplo 2013-0967 Italy
Other privateAlpha-1 Foundation project grant to James Irving United States
Other governmentUCLH/NIHR Biomedical Research Centre United Kingdom
CitationJournal: JCI Insight / Year: 2020
Title: Intrahepatic heteropolymerization of M and Z alpha-1-antitrypsin.
Authors: Laffranchi, M. / Elliston, E.L. / Miranda, E. / Perez, J. / Ronzoni, R. / Jagger, A.M. / Heyer-Chauhan, N. / Brantly, M.L. / Fra, A. / Lomas, D.A. / Irving, J.A.
History
DepositionOct 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
H: FAB 2H2 heavy chain
L: FAB 2H2 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4359
Polymers46,9412
Non-polymers4937
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-88 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.198, 99.198, 80.073
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11L-320-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody FAB 2H2 heavy chain


Mass: 23129.936 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 2H2 light chain


Mass: 23811.256 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

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Non-polymers , 4 types, 372 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.44 Å3/Da / Density % sol: 49.68 % / Description: Bladed
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 3350, 0.2M Ammonium Sulfate, 0.1M Bis-Tris pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2018
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.93→85.91 Å / Num. obs: 665286 / % possible obs: 100 % / Redundancy: 19.2 % / Biso Wilson estimate: 29.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.043 / Rrim(I) all: 0.191 / Χ2: 0.95 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-1.9619.42.3421.425050.5740.7772.4680.94100
1.96-218.81.669224770.7080.5641.7630.94100
2-2.0419.81.3472.524090.770.4411.4170.95100
2.04-2.0819.51.095323270.8220.3621.1540.96100
2.08-2.1218.50.913.522630.8620.310.9620.97100
2.12-2.1719.60.7624.221900.8720.250.8030.95100
2.17-2.2318.80.6474.821000.8860.2190.6830.97100
2.23-2.2919.70.5365.920400.9220.1760.5640.98100
2.29-2.3619.70.4536.819740.9410.1480.4770.97100
2.36-2.4318.70.3368.718520.9540.1130.3550.98100
2.43-2.5219.30.26510.917870.9690.0870.2790.99100
2.52-2.62190.1941517000.9740.0650.2051.04100
2.62-2.7420.10.14320.215960.9810.0460.151.06100
2.74-2.8819.80.1124.914900.9890.0360.1161.05100
2.88-3.0618.80.08928.813860.9920.030.0941.01100
3.06-3.318.90.07534.112430.9960.0250.0790.99100
3.3-3.63200.06339.411160.9980.020.0660.88100
3.63-4.1618.30.065329480.9990.0210.0680.7100
4.16-5.2418.40.059307520.9990.0190.0620.56100
5.24-85.9917.40.04137.44480.9990.0130.0430.74100

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Processing

Software
NameVersionClassification
xia21.10.2-g9c23cb36c-releasedata reduction
xia21.10.2-g9c23cb36c-releasedata scaling
Aimless0.7.1data scaling
PHASER2.8.1phasing
PHENIX1.13-2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AE6

1ae6


Resolution: 1.93→85.91 Å / SU ML: 0.2428 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3933
RfactorNum. reflection% reflection
Rfree0.2352 1655 4.79 %
Rwork0.1986 --
obs0.2004 34552 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.38 Å2
Refinement stepCycle: LAST / Resolution: 1.93→85.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3197 0 26 365 3588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573335
X-RAY DIFFRACTIONf_angle_d0.74974565
X-RAY DIFFRACTIONf_chiral_restr0.0499514
X-RAY DIFFRACTIONf_plane_restr0.0053577
X-RAY DIFFRACTIONf_dihedral_angle_d15.35231176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.990.30531550.26772674X-RAY DIFFRACTION99.65
1.99-2.050.3131280.2582729X-RAY DIFFRACTION100
2.05-2.120.2771320.24032705X-RAY DIFFRACTION99.79
2.12-2.210.30571440.23592694X-RAY DIFFRACTION100
2.21-2.310.27931250.2322738X-RAY DIFFRACTION99.97
2.31-2.430.28061170.22572735X-RAY DIFFRACTION99.93
2.43-2.580.28681230.22682732X-RAY DIFFRACTION99.86
2.58-2.780.25761530.21742718X-RAY DIFFRACTION100
2.78-3.060.26521710.20592712X-RAY DIFFRACTION99.97
3.06-3.510.2191420.18352767X-RAY DIFFRACTION100
3.51-4.420.17781390.15992780X-RAY DIFFRACTION100
4.42-85.990.1981260.18092913X-RAY DIFFRACTION99.97

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