+Open data
-Basic information
Entry | Database: PDB / ID: 1ryo | ||||||
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Title | Human serum transferrin, N-lobe bound with oxalate | ||||||
Components | Serotransferrin | ||||||
Keywords | METAL TRANSPORT / Iron transport | ||||||
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 / 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 / basal plasma membrane / ferric iron binding / osteoclast differentiation / actin filament organization / Post-translational protein phosphorylation / ferrous iron binding / clathrin-coated endocytic vesicle membrane / Iron uptake and transport / regulation of protein stability / regulation of iron ion transport / HFE-transferrin receptor complex / cellular response to iron ion / 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 / antibacterial humoral response / iron ion transport / cytoplasmic vesicle / blood microparticle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Halbrooks, P.J. / Mason, A.B. / Adams, T.E. / Briggs, S.K. / Everse, S.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: The oxalate effect on release of iron from human serum transferrin explained. Authors: Halbrooks, P.J. / Mason, A.B. / Adams, T.E. / Briggs, S.K. / Everse, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ryo.cif.gz | 87.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ryo.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ryo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/1ryo ftp://data.pdbj.org/pub/pdb/validation_reports/ry/1ryo | HTTPS FTP |
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-Related structure data
Related structure data | 1a8eS 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: 36214.250 Da / Num. of mol.: 1 / Fragment: N-terminal lobe (residues 20-346) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TF / Organ (production host): kidney / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P02787 |
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#2: Chemical | ChemComp-OXL / |
#3: Chemical | ChemComp-FE / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 48.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7 Details: 0.2M K-Acetate, 10mM KCl, 20% PEG 3350, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.935 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 27, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.935 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30 Å / Num. all: 108413 / Num. obs: 101890 / % possible obs: 94 % / Rsym value: 0.061 |
Reflection shell | Resolution: 1.2→1.24 Å / % possible all: 86.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1A8E Resolution: 1.2→30 Å / σ(F): 0
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.2→30 Å
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Refine LS restraints |
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Xplor file |
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