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- PDB-4x1d: Ytterbium-bound human serum transferrin -

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Basic information

Entry
Database: PDB / ID: 4x1d
TitleYtterbium-bound human serum transferrin
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / Transferrin / ytterbium / ferric / malonate
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) / Cargo recognition for clathrin-mediated endocytosis / late endosome / 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
MALONATE ION / YTTERBIUM (III) ION / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWang, M. / Zhang, H. / Sun, H.
Funding support Hong Kong, China, 2items
OrganizationGrant numberCountry
Research Grant Council705310P Hong Kong
Shenzhen Municipal governmentZDSYS20140509142721429 China
CitationJournal: Chem.Commun.(Camb.) / Year: 2015
Title: "Anion clamp" allows flexible protein to impose coordination geometry on metal ions
Authors: Wang, M. / Lai, T.P. / Wang, L. / Zhang, H. / Yang, N. / Sadler, P.J. / Sun, H.
History
DepositionNov 24, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_nat / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)151,3038
Polymers150,5692
Non-polymers7346
Water2,504139
1
A: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6524
Polymers75,2841
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-8 kcal/mol
Surface area28690 Å2
MethodPISA
2
B: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6524
Polymers75,2841
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-8 kcal/mol
Surface area28670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.502, 136.863, 107.843
Angle α, β, γ (deg.)90.000, 90.410, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 3 - 679 / Label seq-ID: 3 - 679

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological unit is a monomer. And there are 2 biological units in the asymmetric unit (chain A and chain B).

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Components

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


Mass: 75284.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: serum / References: UniProt: P02787
#2: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Yb
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE IS NATURAL VARIANT.

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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: 3.95 Å3/Da / Density % sol: 68.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M PIPES, 17% PEG3350, 18% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 56472 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.05 / Rrim(I) all: 0.103 / Χ2: 0.817 / Net I/av σ(I): 13.992 / Net I/σ(I): 8.7 / Num. measured all: 235196
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.94.10.76356440.7750.4270.8760.88399.9
2.9-3.024.10.57356280.8510.3210.6580.88199.8
3.02-3.154.20.41756320.8920.2330.4780.92199.9
3.15-3.324.20.24456170.9540.1370.2810.90299.9
3.32-3.534.20.16656400.9710.0930.1910.96599.9
3.53-3.84.20.11456610.980.0630.131.02599.9
3.8-4.184.10.07356700.990.0410.0830.83999.8
4.18-4.7940.04856160.9930.0270.0550.64899.4
4.79-6.034.30.04156950.9940.0230.0470.52100
6.03-504.20.03856690.9950.0210.0430.59898.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QYT

3qyt


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.2167 / WRfactor Rwork: 0.1876 / FOM work R set: 0.8281 / SU B: 11.801 / SU ML: 0.221 / SU R Cruickshank DPI: 0.6082 / SU Rfree: 0.3018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.608 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 2627 4.9 %RANDOM
Rwork0.1983 50792 --
obs0.1998 50792 95.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 123.65 Å2 / Biso mean: 53.457 Å2 / Biso min: 17.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å2-0.06 Å2
2--0.21 Å20 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10214 0 28 139 10381
Biso mean--43.76 40.25 -
Num. residues----1316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910521
X-RAY DIFFRACTIONr_bond_other_d0.0020.029979
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.95714204
X-RAY DIFFRACTIONr_angle_other_deg0.867322828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61551310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49324.419473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.209151785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7361551
X-RAY DIFFRACTIONr_chiral_restr0.0770.21509
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111912
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022387
X-RAY DIFFRACTIONr_mcbond_it3.1075.0885258
X-RAY DIFFRACTIONr_mcbond_other3.1015.0875257
X-RAY DIFFRACTIONr_mcangle_it5.0347.626559
Refine LS restraints NCS

Ens-ID: 1 / Number: 41308 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 105 -
Rwork0.278 2331 -
all-2436 -
obs--59.4 %

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