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- PDB-2hav: Apo-Human Serum Transferrin (Glycosylated) -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2hav
TitleApo-Human Serum Transferrin (Glycosylated)
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / Serotransferrin / human / iron transporter / apo / iron-free
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 / ferric iron binding / osteoclast differentiation / basal plasma membrane / cellular response to iron ion / actin filament organization / Iron uptake and transport / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / regulation of protein stability / ferrous iron binding / regulation of iron ion transport / HFE-transferrin receptor complex / 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 / iron ion transport / antibacterial humoral response / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / early endosome / blood microparticle / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / 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-like domain / Transferrin / 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-like domain / Transferrin / 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
CITRIC ACID / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWally, J. / Everse, S.J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Crystal Structure of Iron-free Human Serum Transferrin Provides Insight into Inter-lobe Communication and Receptor Binding.
Authors: Wally, J. / Halbrooks, P.J. / Vonrhein, C. / Rould, M.A. / Everse, S.J. / Mason, A.B. / Buchanan, S.K.
History
DepositionJun 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serotransferrin
B: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,66013
Polymers149,9462
Non-polymers1,71311
Water00
1
A: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8267
Polymers74,9731
Non-polymers8536
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8346
Polymers74,9731
Non-polymers8615
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.324, 103.258, 200.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer.

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Components

#1: Protein Serotransferrin / Transferrin / Siderophilin / Beta-1-metal-binding globulin


Mass: 74973.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02787
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3

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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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30 mg/ml protein, 0.2 M ammonium citrate pH 7.0, 20% PEG-3350, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 49871 / % possible obs: 96.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.068
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2 / % possible all: 90.5

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Processing

Software
NameClassification
HKL-2000data reduction
PHASERphasing
REFMACrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: human apo-N-lobe structure (1BP5) and the rabbit holo-C1-subdomain (residues 342 to 424 and 579 to 676 from 1JNF)

1bp5

1jnf


Resolution: 2.7→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.293 2094 RANDOM
Rwork0.232 --
all0.232 41336 -
obs0.232 39242 -
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10486 0 115 0 10601
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d1.57
X-RAY DIFFRACTIONp_bond_d0.009

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