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- PDB-1ryo: Human serum transferrin, N-lobe bound with oxalate -

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Basic information

Entry
Database: PDB / ID: 1ryo
TitleHuman serum transferrin, N-lobe bound with oxalate
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / 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
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
: / OXALATE ION / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHalbrooks, P.J. / Mason, A.B. / Adams, T.E. / Briggs, S.K. / Everse, S.J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The oxalate effect on release of iron from human serum transferrin explained.
Authors: Halbrooks, P.J. / Mason, A.B. / Adams, T.E. / Briggs, S.K. / Everse, S.J.
History
DepositionDec 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3583
Polymers36,2141
Non-polymers1442
Water8,953497
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.092, 57.252, 135.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serotransferrin / Transferrin / Siderophilin / Beta-1-metal binding globulin / PRO1400


Mass: 36214.250 Da / Num. of mol.: 1 / Fragment: N-terminal lobe (residues 20-346)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TF / Organ (production host): kidney / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P02787
#2: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 0.2M K-Acetate, 10mM KCl, 20% PEG 3350, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.935 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 27, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.935 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 108413 / Num. obs: 101890 / % possible obs: 94 % / Rsym value: 0.061
Reflection shellResolution: 1.2→1.24 Å / % possible all: 86.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A8E
Resolution: 1.2→30 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 10202 -random
Rwork0.221 ---
all-108413 --
obs-101890 94 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.199 Å20 Å20 Å2
2--0.224 Å20 Å2
3---0.975 Å2
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2527 0 7 497 3031
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it0.5311.5
X-RAY DIFFRACTIONc_mcangle_it0.8822
X-RAY DIFFRACTIONc_scbond_it1.0392
X-RAY DIFFRACTIONc_scangle_it1.6032.5
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.84
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3oxalate.paramoxalate.top
X-RAY DIFFRACTION4fe3.paramfe3.top

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