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- PDB-1b3e: HUMAN SERUM TRANSFERRIN, N-TERMINAL LOBE, EXPRESSED IN PICHIA PASTORIS -

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Basic information

Entry
Database: PDB / ID: 1b3e
TitleHUMAN SERUM TRANSFERRIN, N-TERMINAL LOBE, EXPRESSED IN PICHIA PASTORIS
ComponentsPROTEIN (SERUM TRANSFERRIN)
KeywordsIRON TRANSPORT / GLYCOPROTEIN / TRANSFERRIN / PICHIA PASTORIS / GLYCOSYLATION
Function / homology
Function and homology information


iron chaperone activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding / basal plasma membrane / osteoclast differentiation / cellular response to iron ion ...iron chaperone activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding / basal plasma membrane / osteoclast differentiation / cellular response to iron ion / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / iron ion transport / Iron uptake and transport / ferrous iron binding / regulation of iron ion transport / HFE-transferrin receptor complex / recycling endosome / regulation of protein stability / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / antibacterial humoral response / late endosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Platelet degranulation / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / cytoplasmic vesicle / secretory granule lumen / blood microparticle / vesicle / transmembrane transporter binding / intracellular iron ion homeostasis / early endosome / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / perinuclear region of cytoplasm / enzyme binding / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Serotransferrin, mammalian / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin ...Serotransferrin, mammalian / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / : / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.5 Å
AuthorsBewley, M.C. / Tam, B.M. / Grewal, J. / He, S. / Shewry, S. / Murphy, M.E.P. / Mason, A.B. / Woodworth, R.C. / Baker, E.N. / Macgillivray, R.T.A.
CitationJournal: Biochemistry / Year: 1999
Title: X-ray crystallography and mass spectroscopy reveal that the N-lobe of human transferrin expressed in Pichia pastoris is folded correctly but is glycosylated on serine-32.
Authors: Bewley, M.C. / Tam, B.M. / Grewal, J. / He, S. / Shewry, S. / Murphy, M.E. / Mason, A.B. / Woodworth, R.C. / Baker, E.N. / MacGillivray, R.T.
History
DepositionDec 9, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 26, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (SERUM TRANSFERRIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6213
Polymers36,5061
Non-polymers1162
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.500, 73.500, 156.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PROTEIN (SERUM TRANSFERRIN)


Mass: 36505.523 Da / Num. of mol.: 1 / Fragment: N-TERMINAL LOBE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P02787
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsCARBONATE ION IS COVALENTLY BOUND TO THE FERRIC ION

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: PROTEIN WAS CRYSTALLIZED FROM 40% (V/V) ETHANOL WITH 50MM SODIUM CACODYLATE, PH 6.25. GROWN IN SITTING DROPS AT 277 K. RESERVOIRS CONTAINED 40% (V/V) ETHANOL, 50MM SODIUM CACODYLATE, PH 5.8 - ...Details: PROTEIN WAS CRYSTALLIZED FROM 40% (V/V) ETHANOL WITH 50MM SODIUM CACODYLATE, PH 6.25. GROWN IN SITTING DROPS AT 277 K. RESERVOIRS CONTAINED 40% (V/V) ETHANOL, 50MM SODIUM CACODYLATE, PH 5.8 - 6.3. PRIOR TO CRYSTALLIZATION, THE PROTEIN WAS DIALYSED AGAINST SODIUM BICARBONATE, PH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Components of the solutions
IDNameCrystal-IDSol-ID
140% (V/V) ETHANOL WITH 50MM SODIUM CACODYLATE, PH 6.25.12
20% (V/V) ETHANOL, 50MM SODIUM CACODYLATE,PH 5.8 - 6.3.12
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
180 mg/mlprotein1drop
2150 mMsodium bicarbonate1drop
340 %(v/v)ethanol1reservoir
450 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 1, 1996
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 15238 / % possible obs: 96.9 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 17
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 4.2 / % possible all: 96
Reflection shell
*PLUS
% possible obs: 96 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1refinement
RefinementMethod to determine structure: OTHER
Starting model: 1A8F (HUMAN TRANSFERRIN N-LOBE)

1a8f


Resolution: 2.5→6 Å / Cross valid method: R-FREE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1069 9 %RANDOM SELECTION
Rwork0.177 ---
obs-13490 96.2 %-
Displacement parametersBiso mean: 38 Å2
Refine analyzeLuzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2558 0 5 64 2627
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS

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