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- PDB-3skp: The structure of apo-human transferrin C-lobe with bound sulfate ions -
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Open data
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Basic information
Entry | Database: PDB / ID: 3skp | ||||||
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Title | The structure of apo-human transferrin C-lobe with bound sulfate ions | ||||||
![]() | Serotransferrin | ||||||
![]() | METAL BINDING PROTEIN / transferrin / iron binding protein / transferrin receptor / TbpA / TbpB | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Noinaj, N. / Steere, A.N. / Mason, A.B. / Buchanan, S.K. | ||||||
![]() | ![]() Title: Structural basis for iron piracy by pathogenic Neisseria. Authors: Noinaj, N. / Easley, N.C. / Oke, M. / Mizuno, N. / Gumbart, J. / Boura, E. / Steere, A.N. / Zak, O. / Aisen, P. / Tajkhorshid, E. / Evans, R.W. / Gorringe, A.R. / Mason, A.B. / Steven, A.C. / Buchanan, S.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 152.4 KB | Display | ![]() |
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PDB format | ![]() | 119 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.7 KB | Display | ![]() |
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Full document | ![]() | 439.4 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v83C ![]() 3v89C ![]() 3v8uC ![]() 3v8xC ![]() 2havS S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 38015.176 Da / Num. of mol.: 1 / Fragment: iron binding protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Sequence details | THIS IS A NATURAL VARIANT ACCORDING TO UNIPROT DATABASE. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.11 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M potassium sulfate, 2.2 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2010 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→36.27 Å / Num. all: 52589 / Num. obs: 52589 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Biso Wilson estimate: 20.76 Å2 / Rsym value: 0.084 / Net I/σ(I): 31.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.832 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2HAV Resolution: 1.7→29.563 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.385 Å2 / ksol: 0.357 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→29.563 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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