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Open data
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Basic information
Entry | Database: PDB / ID: 1jqf | ||||||
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Title | Human Transferrin N-Lobe Mutant H249Q | ||||||
![]() | TRANSFERRIN | ||||||
![]() | TRANSPORT PROTEIN / iron binding protein | ||||||
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 | ![]() ![]() | ||||||
![]() | Baker, H.M. / Mason, A.B. / He, Q.-Y. / MacGillivray, R.T.A. / Baker, E.N. | ||||||
![]() | ![]() Title: Ligand variation in the transferrin family: the crystal structure of the H249Q mutant of the human transferrin N-lobe as a model for iron binding in insect transferrins. Authors: Baker, H.M. / Mason, A.B. / He, Q.Y. / MacGillivray, R.T. / 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 | ![]() | 80.5 KB | Display | ![]() |
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PDB format | ![]() | 59.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429 KB | Display | ![]() |
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Full document | ![]() | 431.7 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1a8eS 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: 36891.945 Da / Num. of mol.: 1 / Fragment: N-TERMINUS (Residues 20-353) / Mutation: H249Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CO3 / |
#3: Chemical | ChemComp-FE / |
#4: Chemical | ChemComp-K / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: Hanging drop. Protein solution 35 mg/ml protein in 0.1M ammonium bicarbonate pH 7.4. Reservoir solution 0.1M potassium acetate, pH 7.4, 20-25% PEG 3350. Equal volumes of protein and ...Details: Hanging drop. Protein solution 35 mg/ml protein in 0.1M ammonium bicarbonate pH 7.4. Reservoir solution 0.1M potassium acetate, pH 7.4, 20-25% PEG 3350. Equal volumes of protein and reservoir solutions mixed., VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||
Crystal grow | *PLUS Details: used microseeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 2000 / Details: mirrors |
Radiation | Monochromator: TR mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. all: 30081 / % possible obs: 99.4 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2847 / % possible all: 96.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 30081 |
Reflection shell | *PLUS % possible obs: 96.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1A8E Resolution: 1.85→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.85→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / Rfactor obs: 0.221 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |