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- PDB-5dyh: Ti(IV) bound human serum transferrin -

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Basic information

Entry
Database: PDB / ID: 5dyh
TitleTi(IV) bound human serum transferrin
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / synergistic ion complex
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
TITANIUM ION / CITRIC ACID / CARBONATE ION / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.682 Å
AuthorsSaxena, M. / Sharma, S. / Noinaj, N. / Parks, T.B. / Tinoco, A.D.
Funding support United States, Puerto Rico, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1SC1CA190504-01 United States
The Puerto Rico Science, Technology, and Research Trust2013-000019Puerto Rico
University of Puerto Rico Score Stabilization GrantPuerto Rico
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Unusual Synergism of Transferrin and Citrate in the Regulation of Ti(IV) Speciation, Transport, and Toxicity.
Authors: Tinoco, A.D. / Saxena, M. / Sharma, S. / Noinaj, N. / Delgado, Y. / Quinones Gonzalez, E.P. / Conklin, S.E. / Zambrana, N. / Loza-Rosas, S.A. / Parks, T.B.
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)156,66517
Polymers154,3362
Non-polymers2,32915
Water00
1
A: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4299
Polymers77,1681
Non-polymers1,2618
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2368
Polymers77,1681
Non-polymers1,0687
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.275, 102.016, 197.899
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 3 - 679 / Label seq-ID: 22 - 698

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

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


Mass: 77167.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TF, PRO1400 / Production host: Oryza sativa (Asian cultivated rice) / References: UniProt: P02787
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C6H8O7
#3: Chemical ChemComp-4TI / TITANIUM ION


Mass: 47.867 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ti
#4: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3

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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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 10-13% PEG3350 100 mM Ammonium Citrate buffer / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. obs: 49580 / % possible obs: 98.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 78.83 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.043 / Rrim(I) all: 0.104 / Χ2: 2.848 / Net I/av σ(I): 33 / Net I/σ(I): 10 / Num. measured all: 288832
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.66-2.765.70.78244760.6850.350.8591.07990.6
2.76-2.875.90.58548500.8480.2540.6391.19997.5
2.87-35.90.43248990.910.1890.4721.35898.4
3-3.155.90.29149420.9550.1270.3181.65298.4
3.15-3.355.90.20749870.9710.0920.2272.1799.3
3.35-3.615.80.15449500.9790.0690.1692.98599
3.61-3.975.80.1250150.9830.0540.1324.01899.4
3.97-4.555.70.09650470.990.0440.1064.86499.6
4.55-5.735.90.08450940.990.0380.0934.66599.7
5.73-505.70.06353200.9960.0290.0694.19799

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HAU

2hau


Resolution: 2.682→49.394 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 3768 4.04 %
Rwork0.2022 89437 -
obs0.2036 93205 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 236.04 Å2 / Biso mean: 98.4805 Å2 / Biso min: 30.43 Å2
Refinement stepCycle: final / Resolution: 2.682→49.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10375 0 206 0 10581
Biso mean--148.72 --
Num. residues----1354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310801
X-RAY DIFFRACTIONf_angle_d0.6714579
X-RAY DIFFRACTIONf_chiral_restr0.0271550
X-RAY DIFFRACTIONf_plane_restr0.0031936
X-RAY DIFFRACTIONf_dihedral_angle_d10.9963897
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7732X-RAY DIFFRACTION5.56TORSIONAL
12B7732X-RAY DIFFRACTION5.56TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6818-2.71580.3634950.31752261235667
2.7158-2.75150.39291310.32763147327890
2.7515-2.78920.33961390.31573242338196
2.7892-2.8290.34421420.31813272341496
2.829-2.87130.33631430.31913342348596
2.8713-2.91610.38351360.29353312344896
2.9161-2.96390.36491370.29983340347797
2.9639-3.0150.31031410.28733311345298
3.015-3.06990.33441440.27473358350297
3.0699-3.12890.36911410.27343312345397
3.1289-3.19270.29291410.27413384352597
3.1927-3.26220.28451420.27723378352099
3.2622-3.3380.34511450.26973354349998
3.338-3.42150.28241400.2613399353998
3.4215-3.5140.35631420.25453346348898
3.514-3.61730.31371390.23993338347798
3.6173-3.73410.25721400.22013408354898
3.7341-3.86750.26751370.21433372350998
3.8675-4.02220.24271420.20023390353298
4.0222-4.20520.24321450.18623387353298
4.2052-4.42680.20441350.16763363349898
4.4268-4.70390.15971440.1573378352299
4.7039-5.06680.17351480.14963436358499
5.0668-5.57610.26011460.17023430357699
5.5761-6.38150.21561430.185634193562100
6.3815-8.03440.18431410.17534233564100
8.0344-49.4020.16611490.15783335348497
Refinement TLS params.Method: refined / Origin x: 8.7569 Å / Origin y: -4.5339 Å / Origin z: 11.9399 Å
111213212223313233
T0.4079 Å2-0.034 Å20.035 Å2-0.3616 Å2-0.015 Å2--0.3565 Å2
L0.6302 °2-0.0695 °20.1341 °2-0.1225 °2-0.053 °2---0.0048 °2
S0.0786 Å °-0.1517 Å °0.116 Å °-0.0722 Å °-0.0152 Å °-0.0123 Å °0.0102 Å °-0.0028 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 679
2X-RAY DIFFRACTION1allB3 - 679
3X-RAY DIFFRACTION1allC12 - 22
4X-RAY DIFFRACTION1allD1 - 2
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF1

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