+Open data
-Basic information
Entry | Database: PDB / ID: 1n84 | ||||||
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Title | HUMAN SERUM TRANSFERRIN, N-LOBE | ||||||
Components | Serotransferrin | ||||||
Keywords | TRANSPORT PROTEIN / 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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Adams, T.E. / Mason, A.B. / He, Q.Y. / Halbrooks, P.J. / Briggs, S.K. / Smith, V.C. / Macgillivray, R.T. / Everse, S.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: THE POSITION OF ARGININE 124 CONTROLS THE RATE OF IRON RELEASE FROM THE N-LOBE OF HUMAN SERUM TRANSFERRIN. A STRUCTURAL STUDY Authors: ADAMS, T.E. / MASON, A.B. / HE, Q.Y. / HALBROOKS, P.J. / BRIGGS, S.K. / SMITH, V.C. / MACGILLIVRAY, R.T. / 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 | 1n84.cif.gz | 80.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n84.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 1n84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/1n84 ftp://data.pdbj.org/pub/pdb/validation_reports/n8/1n84 | HTTPS FTP |
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-Related structure data
Related structure data | 1n7wC 1n7xC 1a8eS C: citing same article (ref.) 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: 36604.660 Da / Num. of mol.: 1 / Fragment: N-TERMINAL LOBE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: BABY / Gene: TF / Plasmid: pNUT / Organ (production host): KIDNEY / Production host: Cricetinae (hamsters) / References: UniProt: P02787 |
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#2: Chemical | ChemComp-CO3 / |
#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: 2.33 Å3/Da / Density % sol: 46.76 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7 Details: 0.2M POTASSIUM ACETATE, 20% PEG 3350, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 26, 2000 / Details: MIRRORS |
Radiation | Monochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. all: 23038 / Num. obs: 20270 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.079 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 9.4 / Num. unique all: 2046 / Rsym value: 0.19 / % possible all: 91.6 |
Reflection | *PLUS Num. obs: 20284 / % possible obs: 88.1 % |
Reflection shell | *PLUS % possible obs: 91.6 % / Num. unique obs: 2046 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A8E Resolution: 2.05→16.54 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.2864 Å2 / ksol: 0.326242 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.3 Å2
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Refine analyze | Luzzati coordinate error free: 0.27 Å / Luzzati sigma a free: 0.19 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→16.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rfree: 0.229 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.12 Å |