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- PDB-1btj: HUMAN SERUM TRANSFERRIN, RECOMBINANT N-TERMINAL LOBE, APO FORM, C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1btj | ||||||
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Title | HUMAN SERUM TRANSFERRIN, RECOMBINANT N-TERMINAL LOBE, APO FORM, CRYSTAL FORM 2 | ||||||
![]() | PROTEIN (SERUM TRANSFERRIN) | ||||||
![]() | METAL TRANSPORT / IRON TRANSPORT / GLYCOPROTEIN / TRANSFERRIN / N-LOBE / IRON-FREE FORM / CONFORMATIONAL CHANGE | ||||||
Function / homology | ![]() iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade ...iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade / ferric iron binding / osteoclast differentiation / basal plasma membrane / cellular response to iron ion / actin filament organization / Iron uptake and transport / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / regulation of protein stability / ferrous iron binding / 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) / late endosome / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / Clathrin-mediated endocytosis / iron ion transport / antibacterial humoral response / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / early endosome / blood microparticle / endosome membrane / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Jeffrey, P.D. / Bewley, M.C. / Macgillivray, R.T.A. / Mason, A.B. / Woodworth, R.C. / Baker, E.N. | ||||||
![]() | ![]() Title: Ligand-induced conformational change in transferrins: crystal structure of the open form of the N-terminal half-molecule of human transferrin. Authors: Jeffrey, P.D. / Bewley, M.C. / MacGillivray, R.T. / Mason, A.B. / Woodworth, R.C. / Baker, E.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.5 KB | Display | ![]() |
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PDB format | ![]() | 97.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 376.4 KB | Display | ![]() |
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Full document | ![]() | 406 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37215.270 Da / Num. of mol.: 2 / Fragment: N-TERMINAL LOBE Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.3 Details: PROTEIN DROP: 20 MG/ML PROTEIN, 20MM NAHCO3, 50 MM KCL. RESERVOIR: 50 MM POTASSIUM ACETATE, PH 5.3, 35% MPD., VAPOR DIFFUSION, SITTING DROP | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 46 % | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 15, 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: 3.2→40 Å / Num. obs: 11269 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 3.2→3.5 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9 |
Reflection shell | *PLUS % possible obs: 99.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: HUMAN TRANSFERRIN N-LOBE, HOLO FORM, INDIVIDUAL DOMAINS Resolution: 3.2→6 Å / Cross valid method: R-FREE / σ(F): 0
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Refine analyze | Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→6 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 6 Å / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.9 |