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Yorodumi- PDB-1fqf: CRYSTAL STRUCTURES OF MUTANT (K296A) THAT ABOLISH THE DILYSINE IN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fqf | ||||||
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Title | CRYSTAL STRUCTURES OF MUTANT (K296A) THAT ABOLISH THE DILYSINE INTERACTION IN THE N-LOBE OF HUMAN TRANSFERRIN | ||||||
Components | SEROTRANSFERRIN | ||||||
Keywords | METAL TRANSPORT / IRON TRANSPORT / TRANSFERRIN / N-LOBE / IRON-RELEASE / DILYSINE INTERACTION | ||||||
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 / Resolution: 2.1 Å | ||||||
Authors | Nurizzo, D. / Baker, H.M. / Baker, E.N. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Crystal structures and iron release properties of mutants (K206A and K296A) that abolish the dilysine interaction in the N-lobe of human transferrin. Authors: Nurizzo, D. / Baker, H.M. / He, Q.Y. / MacGillivray, R.T. / Mason, A.B. / Woodworth, R.C. / Baker, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fqf.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fqf.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 1fqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/1fqf ftp://data.pdbj.org/pub/pdb/validation_reports/fq/1fqf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer constituted by two domains in between the iron and its carbonate counterpart are linked. |
-Components
#1: Protein | Mass: 36546.559 Da / Num. of mol.: 1 / Fragment: N-LOBE / Mutation: K296A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue fraction: SERUM / Plasmid: PNUT-BHK / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P02787 |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-CO3 / |
#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: 2.28 Å3/Da / Density % sol: 46.03 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 18% PolyEthyleneGlycol 3350, 100mM Potassium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 17, 2000 |
Radiation | 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→15 Å / Num. all: 19129 / Num. obs: 19129 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.2 / Redundancy: 2.9 % / Biso Wilson estimate: 33.033 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.301 / Num. unique all: 4750 / % possible all: 87.1 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 87.1 % / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Resolution: 2.1→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 15 Å / σ(F): 0 / Num. reflection Rfree: 1055 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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