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Yorodumi- PDB-6i3z: Fab fragment of an antibody selective for wild-type alpha-1-antit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i3z | |||||||||||||||
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Title | Fab fragment of an antibody selective for wild-type alpha-1-antitrypsin in complex with its antigen | |||||||||||||||
Components |
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Keywords | PROTEIN BINDING / Antibody fragment / Antitrypsin binding / Diagnostic / Monoclonal / selective / wild-type / Glu342 / E342 | |||||||||||||||
Function / homology | Function and homology information Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / serine-type endopeptidase inhibitor activity / blood coagulation ...Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / serine-type endopeptidase inhibitor activity / blood coagulation / Platelet degranulation / protease binding / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å | |||||||||||||||
Authors | Laffranchi, M. / Elliston, E.L.K. / Miranda, E. / Perez, J. / Jagger, A.M. / Fra, A. / Lomas, D.A. / Irving, J.A. | |||||||||||||||
Funding support | United Kingdom, Italy, United States, 4items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i3z.cif.gz | 159.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i3z.ent.gz | 118.7 KB | Display | PDB format |
PDBx/mmJSON format | 6i3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i3z_validation.pdf.gz | 459.9 KB | Display | wwPDB validaton report |
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Full document | 6i3z_full_validation.pdf.gz | 466.2 KB | Display | |
Data in XML | 6i3z_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 6i3z_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/6i3z ftp://data.pdbj.org/pub/pdb/validation_reports/i3/6i3z | HTTPS FTP |
-Related structure data
Related structure data | 6i1oC 1ezxS 6io1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Antibody , 2 types, 2 molecules HL
#3: Antibody | 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 |
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#4: Antibody | Mass: 23914.398 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 |
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 40018.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): XL1-Blue / References: UniProt: P01009 |
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#2: Protein/peptide | Mass: 4681.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): XL-1 Blue / References: UniProt: P01009 |
-Non-polymers , 3 types, 35 molecules
#5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.12 % / Description: Plate |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 0.1 M ammonium sulfate, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2018 / Details: Toroidal mirror | ||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 3.1→37.82 Å / Num. obs: 13004 / % possible obs: 92.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 51.51 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.127 / Rrim(I) all: 0.226 / Net I/σ(I): 3.4 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IO1,1EZX Resolution: 3.1→37.82 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 30.66
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.54 Å2 / Biso mean: 39.7541 Å2 / Biso min: 2.68 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→37.82 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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