[English] 日本語
Yorodumi- PDB-1fqe: CRYSTAL STRUCTURES OF MUTANT (K206A) THAT ABOLISH THE DILYSINE IN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fqe | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURES OF MUTANT (K206A) 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 / SYNCHROTRON / Resolution: 1.8 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fqe.cif.gz | 84.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fqe.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/1fqe ftp://data.pdbj.org/pub/pdb/validation_reports/fq/1fqe | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
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: K206A 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 |
---|---|
#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-CO3 / |
#4: Chemical | ChemComp-K / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.38 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 20-25% PolyEthyleneGlycol 3350, 100mM Potassium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 11, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→14.73 Å / Num. all: 373302 / Num. obs: 29721 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.4 / Redundancy: 3.1 % / Biso Wilson estimate: 9 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.185 / Num. unique all: 10127 / % possible all: 82.1 |
Reflection | *PLUS Num. measured all: 373302 |
Reflection shell | *PLUS % possible obs: 82.1 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→14.73 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.0949 Å2 / ksol: 0.288978 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.7 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→14.73 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / σ(F): 0 / % reflection Rfree: 4 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.7 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.251 / % reflection Rfree: 3.8 % / Rfactor Rwork: 0.252 |