+Open data
-Basic information
Entry | Database: PDB / ID: 4hgk | ||||||
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Title | Shark IgNAR variable domain | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Ig-fold / human albumin | ||||||
Function / homology | Function and homology information cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / small molecule binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Squalus acanthias (spiny dogfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å | ||||||
Authors | Olland, A.O. / Kovalenko, O.V. / Svenson, K. / King, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Atypical Antigen Recognition Mode of a Shark Immunoglobulin New Antigen Receptor (IgNAR) Variable Domain Characterized by Humanization and Structural Analysis. Authors: Kovalenko, O.V. / Olland, A. / Piche-Nicholas, N. / Godbole, A. / King, D. / Svenson, K. / Calabro, V. / Muller, M.R. / Barelle, C.J. / Somers, W. / Gill, D.S. / Mosyak, L. / Tchistiakova, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hgk.cif.gz | 239.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hgk.ent.gz | 192.9 KB | Display | PDB format |
PDBx/mmJSON format | 4hgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hgk_validation.pdf.gz | 457.7 KB | Display | wwPDB validaton report |
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Full document | 4hgk_full_validation.pdf.gz | 483.5 KB | Display | |
Data in XML | 4hgk_validation.xml.gz | 43.4 KB | Display | |
Data in CIF | 4hgk_validation.cif.gz | 58.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/4hgk ftp://data.pdbj.org/pub/pdb/validation_reports/hg/4hgk | HTTPS FTP |
-Related structure data
Related structure data | 4hgmC 1ha2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 66571.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02768 #2: Protein | Mass: 14153.843 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Squalus acanthias (spiny dogfish) / Cell line (production host): COS-1 / Production host: Chlorocebus aethiops (grivet) #3: 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: 2.22 Å3/Da / Density % sol: 44.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 16% PEG 2000 MME, 100 mM sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.04→52.055 Å / Num. all: 25935 / Num. obs: 25935 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 74.74 Å2 / Rmerge(I) obs: 0.22 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HA2 Resolution: 3.04→52.055 Å / Cor.coef. Fo:Fc: 0.8831 / Cor.coef. Fo:Fc free: 0.8542 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 85.54 Å2
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Refine analyze | Luzzati coordinate error obs: 0.68 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.04→52.055 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.04→3.16 Å / Total num. of bins used: 13
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