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Open data
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Basic information
Entry | Database: PDB / ID: 1n7x | ||||||
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Title | HUMAN SERUM TRANSFERRIN, N-LOBE Y45E MUTANT | ||||||
![]() | Serotransferrin | ||||||
![]() | TRANSPORT PROTEIN / IRON TRANSPORT | ||||||
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 / actin filament organization / cellular response to iron ion / Post-translational protein phosphorylation / Iron uptake and transport / clathrin-coated endocytic vesicle membrane / 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) / 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 / blood microparticle / early endosome / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Adams, T.E. / Mason, A.B. / He, Q.Y. / Halbrooks, P.J. / Briggs, S.K. / Smith, V.C. / Macgillivray, R.T. / Everse, S.J. | ||||||
![]() | ![]() Title: THE POSITION OF ARGININE 124 CONTROLS THE RATE OF IRON RELEASE FROM THE N-LOBE OF HUMAN SERUM TRANSFERRIN. A STRUCTURAL STUDY Authors: ADAMS, T.E. / MASON, A.B. / HE, Q.Y. / HALBROOKS, P.J. / BRIGGS, S.K. / SMITH, V.C. / MACGILLIVRAY, R.T. / EVERSE, S.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.7 KB | Display | ![]() |
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PDB format | ![]() | 60.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1n7wC ![]() 1n84C ![]() 1a8eS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36570.598 Da / Num. of mol.: 1 / Fragment: N-TERMINAL LOBE / Mutation: Y45E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-CO3 / |
#3: Chemical | ChemComp-FE / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 43.94 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7 Details: 0.2M POTASSIUM ACETATE, 20% PEG 3350, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 20, 2000 / Details: MIRRORS |
Radiation | Monochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 20664 / Num. obs: 19129 / % possible obs: 92.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.062 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 11 / Num. unique all: 1813 / Rsym value: 0.144 / % possible all: 90.2 |
Reflection | *PLUS Lowest resolution: 30 Å / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 90.2 % / Num. unique obs: 1813 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A8E Resolution: 2.1→14 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.3392 Å2 / ksol: 0.363566 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.1 Å2
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Refine analyze | Luzzati coordinate error free: 0.29 Å / Luzzati sigma a free: 0.18 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.242 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.18 Å |