+Open data
-Basic information
Entry | Database: PDB / ID: 6wio | ||||||
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Title | Fab antigen complex | ||||||
Components |
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Keywords | CYTOKINE/IMMUNE SYSTEM / Fab / Il-17 / CYTOKINE / CYTOKINE-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / cell death / positive regulation of chemokine (C-X-C motif) ligand 1 production ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / cell death / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / positive regulation of bicellular tight junction assembly / fibroblast activation / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / keratinocyte proliferation / cellular response to interleukin-1 / defense response to fungus / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / cytokine activity / response to wounding / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / cell-cell signaling / gene expression / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / inflammatory response / immune response / protein heterodimerization activity / external side of plasma membrane / innate immune response / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | Antonysamy, S. | ||||||
Citation | Journal: Plos One / Year: 2020 Title: Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing. Authors: Lieu, R. / Antonysamy, S. / Druzina, Z. / Ho, C. / Kang, N.R. / Pustilnik, A. / Wang, J. / Atwell, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wio.cif.gz | 229.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wio.ent.gz | 184.6 KB | Display | PDB format |
PDBx/mmJSON format | 6wio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wio_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 6wio_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 6wio_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 6wio_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/6wio ftp://data.pdbj.org/pub/pdb/validation_reports/wi/6wio | HTTPS FTP |
-Related structure data
Related structure data | 6wg8C 6wgbC 6wgjC 6wgkC 6wglC 6wirC 5vb9S 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
#1: Antibody | Mass: 25036.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified baculovirus |
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#2: Antibody | Mass: 23172.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified baculovirus |
#3: Protein | Mass: 18356.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Production host: unidentified baculovirus / References: UniProt: Q16552 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.42 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 3350 + 200mM Ammonium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→79.1 Å / Num. obs: 46955 / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.17→2.28 Å / Num. unique obs: 88363 / Rpim(I) all: 0.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VB9 Resolution: 2.17→79.1 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.15
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Displacement parameters | Biso max: 233.06 Å2 / Biso mean: 69.14 Å2 / Biso min: 38.4 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.17→79.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.17→2.19 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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