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- PDB-4x1b: Human serum transferrin with ferric ion bound at the C-lobe only -

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Basic information

Entry
Database: PDB / ID: 4x1b
TitleHuman serum transferrin with ferric ion bound at the C-lobe only
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 / positive regulation of phosphorylation / clathrin-coated pit / 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 / positive regulation of phosphorylation / clathrin-coated pit / ERK1 and ERK2 cascade / osteoclast differentiation / ferric iron binding / basal plasma membrane / actin filament organization / cellular response to iron ion / Post-translational protein phosphorylation / Iron uptake and transport / clathrin-coated endocytic vesicle membrane / ferrous iron binding / regulation of protein stability / regulation of iron ion transport / HFE-transferrin receptor complex / recycling endosome / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / late endosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / antibacterial humoral response / Clathrin-mediated endocytosis / iron ion transport / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / blood microparticle / transmembrane transporter binding / early endosome / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / 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 / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsWang, M. / Zhang, H. / Sun, H.
Funding support Hong Kong, China, 2items
OrganizationGrant numberCountry
Research Grant Council705210P 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
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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)75,5344
Polymers75,2841
Non-polymers2503
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-10 kcal/mol
Surface area28810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.056, 156.649, 107.162
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-832-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Serotransferrin / Fe-hTF / 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) / Organ: serum / References: UniProt: P02787
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MLI / MALONATE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 3.99 Å3/Da / Density % sol: 69.16 %
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: 0.97852 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 42808 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.03 / Rrim(I) all: 0.081 / Χ2: 0.915 / Net I/av σ(I): 24.179 / Net I/σ(I): 10.4 / Num. measured all: 315885
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.547.50.73742100.9050.2890.7920.928100
2.54-2.647.50.53242150.9470.2090.5720.913100
2.64-2.767.50.37142560.9720.1450.3990.891100
2.76-2.97.50.23842570.9850.0930.2550.86100
2.9-3.097.50.16742320.990.0660.180.879100
3.09-3.327.40.11542790.9920.0450.1241.041100
3.32-3.667.40.0942720.9920.0350.0971.26100
3.66-4.197.30.06642980.9950.0260.0711.178100
4.19-5.287.10.0443400.9980.0160.0430.648100
5.28-507.20.03744490.9970.0150.040.55299

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Processing

Software
NameVersionClassification
DENZOdata collection
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: 2.45→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2258 / WRfactor Rwork: 0.1881 / FOM work R set: 0.8433 / SU B: 12.517 / SU ML: 0.147 / SU R Cruickshank DPI: 0.2578 / SU Rfree: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 2074 5 %RANDOM
Rwork0.19 39358 --
obs0.1918 39358 97.06 %-
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: 121.29 Å2 / Biso mean: 55.587 Å2 / Biso min: 26.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0 Å2
2--0.15 Å20 Å2
3---0.65 Å2
Refinement stepCycle: final / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5045 0 14 230 5289
Biso mean--50.31 48.53 -
Num. residues----650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195190
X-RAY DIFFRACTIONr_bond_other_d0.0010.024837
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.9587009
X-RAY DIFFRACTIONr_angle_other_deg0.778311185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1195646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96224.464233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0215884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2971525
X-RAY DIFFRACTIONr_chiral_restr0.0680.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215882
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021173
X-RAY DIFFRACTIONr_mcbond_it1.1892.8882596
X-RAY DIFFRACTIONr_mcbond_other1.1882.8872595
X-RAY DIFFRACTIONr_mcangle_it1.9674.3253238
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 114 -
Rwork0.227 2208 -
all-2322 -
obs--75.37 %
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)
13.10280.91470.7183.03950.79653.15270.0520.29130.0885-0.1602-0.0002-0.0142-0.27540.1876-0.05180.11060.02950.02890.08570.01290.009415.626810.615-13.1781
20.52640.32890.50231.6320.44943.50490.11670.00080.082-0.009-0.08210.0529-0.19880.04-0.03460.079-0.01690.04660.0629-0.00620.036314.576517.98798.7062
35.20050.2688-0.2973.8385-0.10413.8770.1335-0.0175-0.19660.1391-0.1031-0.757-0.11290.7466-0.03040.3843-0.25730.07890.39860.03130.26140.312334.40491.6183
44.5980.7661-0.88472.7167-0.0373.29840.219-0.06120.43960.5354-0.14720.4813-0.2656-0.2652-0.07180.4049-0.16740.06660.17960.05220.173834.860655.9308-14.187
53.73740.58060.18453.87440.03972.57330.0939-0.16570.43980.3835-0.0065-0.2188-0.55180.3917-0.08740.5316-0.25920.14050.40390.00330.232833.641641.3963.9294
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 92
2X-RAY DIFFRACTION2A93 - 333
3X-RAY DIFFRACTION3A339 - 412
4X-RAY DIFFRACTION4A413 - 583
5X-RAY DIFFRACTION5A584 - 679

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