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- PDB-3skp: The structure of apo-human transferrin C-lobe with bound sulfate ions -

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Basic information

Entry
Database: PDB / ID: 3skp
TitleThe structure of apo-human transferrin C-lobe with bound sulfate ions
ComponentsSerotransferrin
KeywordsMETAL BINDING PROTEIN / transferrin / iron binding protein / transferrin receptor / TbpA / TbpB
Function / homology
Function and homology information


iron chaperone activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding / basal plasma membrane / osteoclast differentiation / cellular response to iron ion ...iron chaperone activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding / basal plasma membrane / osteoclast differentiation / cellular response to iron ion / Post-translational protein phosphorylation / iron ion transport / Iron uptake and transport / clathrin-coated endocytic vesicle membrane / regulation of iron ion transport / ferrous iron binding / HFE-transferrin receptor complex / recycling endosome / regulation of protein stability / 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) / antibacterial humoral response / late endosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Platelet degranulation / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / cytoplasmic vesicle / secretory granule lumen / blood microparticle / vesicle / transmembrane transporter binding / intracellular iron ion homeostasis / early endosome / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / 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 / Transferrin-like domain / 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 / Transferrin-like domain / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNoinaj, N. / Steere, A.N. / Mason, A.B. / Buchanan, S.K.
CitationJournal: Nature / Year: 2012
Title: Structural basis for iron piracy by pathogenic Neisseria.
Authors: Noinaj, N. / Easley, N.C. / Oke, M. / Mizuno, N. / Gumbart, J. / Boura, E. / Steere, A.N. / Zak, O. / Aisen, P. / Tajkhorshid, E. / Evans, R.W. / Gorringe, A.R. / Mason, A.B. / Steven, A.C. / Buchanan, S.K.
History
DepositionJun 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Mar 14, 2012Group: Database references
Revision 1.4Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 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)38,7849
Polymers38,0151
Non-polymers7698
Water6,666370
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serotransferrin
hetero molecules

A: Serotransferrin
hetero molecules

A: Serotransferrin
hetero molecules

A: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,13536
Polymers152,0614
Non-polymers3,07432
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area13170 Å2
ΔGint-473 kcal/mol
Surface area54290 Å2
MethodPISA
3
A: Serotransferrin
hetero molecules

A: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,56718
Polymers76,0302
Non-polymers1,53716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area4930 Å2
ΔGint-230 kcal/mol
Surface area28800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.847, 95.847, 204.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-283-

HOH

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Components

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


Mass: 38015.176 Da / Num. of mol.: 1 / Fragment: iron binding protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TF, PRO1400 / Cell (production host): baby hamster kidney (BHK) cells / Production host: Cricetinae (hamsters) / References: UniProt: P02787
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS IS A NATURAL VARIANT ACCORDING TO UNIPROT DATABASE.

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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: 3.08 Å3/Da / Density % sol: 60.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M potassium sulfate, 2.2 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→36.27 Å / Num. all: 52589 / Num. obs: 52589 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Biso Wilson estimate: 20.76 Å2 / Rsym value: 0.084 / Net I/σ(I): 31.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.832 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HAV

2hav


Resolution: 1.7→29.563 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 2685 5.11 %random
Rwork0.176 ---
obs0.1771 52589 99.9 %-
all-52589 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.385 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0553 Å20 Å20 Å2
2--0.0553 Å20 Å2
3----0.1106 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 40 370 3002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062688
X-RAY DIFFRACTIONf_angle_d1.0033623
X-RAY DIFFRACTIONf_dihedral_angle_d11.404962
X-RAY DIFFRACTIONf_chiral_restr0.073388
X-RAY DIFFRACTIONf_plane_restr0.004467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73010.29751410.27272567X-RAY DIFFRACTION99
1.7301-1.76340.27541490.25992575X-RAY DIFFRACTION100
1.7634-1.79940.29571520.24092566X-RAY DIFFRACTION100
1.7994-1.83850.25311410.23682593X-RAY DIFFRACTION100
1.8385-1.88130.25251390.20712610X-RAY DIFFRACTION100
1.8813-1.92830.24061500.19942563X-RAY DIFFRACTION100
1.9283-1.98050.2031330.18412601X-RAY DIFFRACTION100
1.9805-2.03870.1891590.17252593X-RAY DIFFRACTION100
2.0387-2.10450.20171150.16772626X-RAY DIFFRACTION100
2.1045-2.17970.18611580.16712579X-RAY DIFFRACTION100
2.1797-2.26690.20431480.16382608X-RAY DIFFRACTION100
2.2669-2.37010.15251190.16062641X-RAY DIFFRACTION100
2.3701-2.4950.19261200.16822644X-RAY DIFFRACTION100
2.495-2.65120.23081300.1852646X-RAY DIFFRACTION100
2.6512-2.85570.23021420.18922643X-RAY DIFFRACTION100
2.8557-3.14280.19751490.18542644X-RAY DIFFRACTION100
3.1428-3.59690.17241410.16132668X-RAY DIFFRACTION100
3.5969-4.52910.16341410.13922704X-RAY DIFFRACTION100
4.5291-29.56780.18141580.17812833X-RAY DIFFRACTION100
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)
10.93220.1015-0.24230.52640.17770.5892-0.0077-0.0446-0.0928-0.0095-0.01960.03920.03650.0530.01860.1226-0.0058-0.00340.10930.01420.14836.7682-26.962-16.1815
20.696-0.30120.8580.5539-0.21840.91280.31580.2486-0.1648-0.1783-0.19770.26450.23210.20180.01260.18940.1003-0.0590.1708-0.05560.1272-16.695-36.3953-35.2548
31.3173-0.14150.03210.42610.0070.3850.00020.00090.09120.0007-0.0138-0.0126-0.0370.07350.01260.1130.00140.00220.1104-0.00340.11922.2326-21.3011-19.0177
40.6372-0.1880.39520.0835-0.19810.37910.1510.0306-0.52240.1217-0.0176-0.01070.2454-0.1443-0.06560.2598-0.0568-0.02090.13630.03470.2981-8.0288-41.5293-13.6105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 339:425)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 426:576)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 577:652)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 653:676)

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