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Yorodumi- PDB-1b3e: HUMAN SERUM TRANSFERRIN, N-TERMINAL LOBE, EXPRESSED IN PICHIA PASTORIS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b3e | ||||||
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Title | HUMAN SERUM TRANSFERRIN, N-TERMINAL LOBE, EXPRESSED IN PICHIA PASTORIS | ||||||
Components | PROTEIN (SERUM TRANSFERRIN) | ||||||
Keywords | IRON TRANSPORT / GLYCOPROTEIN / TRANSFERRIN / PICHIA PASTORIS / GLYCOSYLATION | ||||||
Function / homology | Function and homology information iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / positive regulation of bone resorption / positive regulation of phosphorylation / endocytic vesicle / basal plasma membrane / clathrin-coated pit ...iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / positive regulation of bone resorption / positive regulation of phosphorylation / endocytic vesicle / basal plasma membrane / clathrin-coated pit / ERK1 and ERK2 cascade / ferric iron binding / osteoclast differentiation / clathrin-coated endocytic vesicle membrane / actin filament organization / cellular response to iron ion / Post-translational protein phosphorylation / Iron uptake and transport / ferrous iron binding / regulation of protein stability / regulation of iron ion transport / HFE-transferrin receptor complex / recycling endosome / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / late endosome / Platelet degranulation / iron ion transport / antibacterial humoral response / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / blood microparticle / endosome membrane / early endosome / apical plasma membrane / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.5 Å | ||||||
Authors | Bewley, M.C. / Tam, B.M. / Grewal, J. / He, S. / Shewry, S. / Murphy, M.E.P. / Mason, A.B. / Woodworth, R.C. / Baker, E.N. / Macgillivray, R.T.A. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: X-ray crystallography and mass spectroscopy reveal that the N-lobe of human transferrin expressed in Pichia pastoris is folded correctly but is glycosylated on serine-32. Authors: Bewley, M.C. / Tam, B.M. / Grewal, J. / He, S. / Shewry, S. / Murphy, M.E. / Mason, A.B. / Woodworth, R.C. / Baker, E.N. / MacGillivray, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b3e.cif.gz | 79.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b3e.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 1b3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b3e_validation.pdf.gz | 379 KB | Display | wwPDB validaton report |
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Full document | 1b3e_full_validation.pdf.gz | 382.2 KB | Display | |
Data in XML | 1b3e_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 1b3e_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/1b3e ftp://data.pdbj.org/pub/pdb/validation_reports/b3/1b3e | HTTPS FTP |
-Related structure data
Related structure data | 1a8fS S: Starting model for refinement |
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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: Protein | Mass: 36505.523 Da / Num. of mol.: 1 / Fragment: N-TERMINAL LOBE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P02787 |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-CO3 / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | CARBONATE ION IS COVALENTLY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 57 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.25 Details: PROTEIN WAS CRYSTALLIZED FROM 40% (V/V) ETHANOL WITH 50MM SODIUM CACODYLATE, PH 6.25. GROWN IN SITTING DROPS AT 277 K. RESERVOIRS CONTAINED 40% (V/V) ETHANOL, 50MM SODIUM CACODYLATE, PH 5.8 - ...Details: PROTEIN WAS CRYSTALLIZED FROM 40% (V/V) ETHANOL WITH 50MM SODIUM CACODYLATE, PH 6.25. GROWN IN SITTING DROPS AT 277 K. RESERVOIRS CONTAINED 40% (V/V) ETHANOL, 50MM SODIUM CACODYLATE, PH 5.8 - 6.3. PRIOR TO CRYSTALLIZATION, THE PROTEIN WAS DIALYSED AGAINST SODIUM BICARBONATE, PH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 1, 1996 |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. obs: 15238 / % possible obs: 96.9 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.5→2.6 Å / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 4.2 / % possible all: 96 |
Reflection shell | *PLUS % possible obs: 96 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: 1A8F (HUMAN TRANSFERRIN N-LOBE) Resolution: 2.5→6 Å / Cross valid method: R-FREE / σ(F): 0
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Displacement parameters | Biso mean: 38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.177 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |