+Open data
-Basic information
Entry | Database: PDB / ID: 6wir | ||||||
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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 / molecular replacement / Resolution: 2.96 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 | 6wir.cif.gz | 224.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wir.ent.gz | 181.4 KB | Display | PDB format |
PDBx/mmJSON format | 6wir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wir_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 6wir_full_validation.pdf.gz | 461.1 KB | Display | |
Data in XML | 6wir_validation.xml.gz | 21 KB | Display | |
Data in CIF | 6wir_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/6wir ftp://data.pdbj.org/pub/pdb/validation_reports/wi/6wir | HTTPS FTP |
-Related structure data
Related structure data | 6wg8C 6wgbC 6wgjC 6wgkC 6wglC 6wioC 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: 26049.090 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: 3.25 Å3/Da / Density % sol: 62.19 % |
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Crystal grow | Temperature: 274 K / Method: vapor diffusion, sitting drop Details: 100mM Hepes pH 7, 15% PEG4K, 200mM Magnesium 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 6M / Detector: PIXEL / Date: Jun 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.96→71.61 Å / Num. obs: 19713 / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2.96→3.12 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2781 / Rpim(I) all: 0.242 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VB9 Resolution: 2.96→71.61 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.726 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.88 / SU Rfree Blow DPI: 0.355 / SU Rfree Cruickshank DPI: 0.351
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Displacement parameters | Biso max: 263.39 Å2 / Biso mean: 111.61 Å2 / Biso min: 61.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.96→71.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.96→2.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 48
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Refinement TLS params. | T11: 0.304 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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