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- PDB-5h52: Structure of Titanium-bound human serum transferrin -

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Basic information

Entry
Database: PDB / ID: 5h52
TitleStructure of Titanium-bound human serum transferrin
ComponentsSerotransferrin
KeywordsMETAL BINDING PROTEIN / transferrin titanium citrate
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 / MALONATE ION / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsCurtin, J.P. / Wang, M. / Sun, H.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University of Hong Kong8100013 Hong Kong
CitationJournal: J. Biol. Inorg. Chem. / Year: 2018
Title: The role of citrate, lactate and transferrin in determining titanium release from surgical devices into human serum.
Authors: Curtin, J.P. / Wang, M. / Cheng, T. / Jin, L. / Sun, H.
History
DepositionNov 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6745
Polymers75,2841
Non-polymers3904
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.977, 156.667, 107.855
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 75284.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02787
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-4TI / TITANIUM ION


Mass: 47.867 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ti
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNATURAL VARIANT AT THIS POSITION

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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: 3.9 Å3/Da / Density % sol: 68.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: PIPES-Na 0.1M, PEG 3350 17%, disodium malonate 8mM, glycerol 18%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.9→103.97 Å / Num. obs: 26553 / % possible obs: 99 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.098 / Net I/av σ(I): 26.111 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.9-2.958.81.6660.685191.8
2.95-310.51.570.741194.6
3-3.0611.91.3350.799196
3.06-3.1212.71.10.869198.6
3.12-3.1913.50.9180.893199.9
3.19-3.2714.30.7110.961100
3.27-3.3514.40.5710.9591100
3.35-3.4414.50.420.9761100
3.44-3.5414.40.3360.9841100
3.54-3.6514.40.2520.991100
3.65-3.7814.30.1960.9931100
3.78-3.9414.40.1610.9951100
3.94-4.1114.40.1180.9971100
4.11-4.3314.30.0930.9971100
4.33-4.614.30.0910.997199.9
4.6-4.9614.30.0850.997199.9
4.96-5.4613.90.080.9961100
5.46-6.2413.70.0580.9981100
6.24-7.8613.60.0410.9991100
7.86-5013.40.0350.999199

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.02 Å41.08 Å
Translation8.02 Å41.08 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.6.1phasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X1B

4x1b


Resolution: 3→103.97 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 19.154 / SU ML: 0.232 / SU R Cruickshank DPI: 0.2587 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.334 / Details: HYDROGENS HAVE BEEN USED
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 1161 5.1 %RANDOM
Rwork0.1697 ---
obs0.1724 21792 95.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 166.14 Å2 / Biso mean: 59.869 Å2 / Biso min: 12.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å2-0 Å2
2---0.59 Å20 Å2
3----0.37 Å2
Refinement stepCycle: final / Resolution: 3→103.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5037 0 22 13 5072
Biso mean--78.08 42.46 -
Num. residues----650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195184
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9577010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.945646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64724.464233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.62215876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6751525
X-RAY DIFFRACTIONr_chiral_restr0.1230.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213933
X-RAY DIFFRACTIONr_mcbond_it7.7215.7942596
X-RAY DIFFRACTIONr_mcangle_it10.6443238
X-RAY DIFFRACTIONr_scbond_it9.9246.0472587
X-RAY DIFFRACTIONr_rigid_bond_restr4.55132618
X-RAY DIFFRACTIONr_sphericity_bonded43.0452550
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 70 -
Rwork0.234 1109 -
all-1179 -
obs--67.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01040.0171-0.01140.0338-0.02670.0246-0.00170.00950.0042-0.00470.00620.00340.00430.0053-0.00450.00080.0009-0.00010.0299-0.00140.033314.884613.5368-10.9335
20.0187-0.0254-0.02530.03770.03830.0393-0.0009-0.0009-0.01020.0073-0.00130.00560.0081-0.0010.00210.0123-0.0046-0.0090.02510.00020.047814.033318.815418.7456
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 92
2X-RAY DIFFRACTION1A247 - 331
3X-RAY DIFFRACTION2A93 - 246

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