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- PDB-2o84: Crystal structure of K206E mutant of N-lobe human transferrin -

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Basic information

Entry
Database: PDB / ID: 2o84
TitleCrystal structure of K206E mutant of N-lobe human transferrin
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / Human transferrin / iron binding and release / dilysine pair
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 / basal plasma membrane / ferric iron binding / osteoclast differentiation / actin filament organization / Post-translational protein phosphorylation / ferrous iron binding / clathrin-coated endocytic vesicle membrane / Iron uptake and transport / regulation of protein stability / regulation of iron ion transport / HFE-transferrin receptor complex / cellular response to iron ion / 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 / antibacterial humoral response / iron ion transport / cytoplasmic vesicle / blood microparticle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / early endosome / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / 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
CARBONATE ION / : / : / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBaker, H.M. / Nurizzo, D. / Mason, A.B. / Baker, E.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structures of two mutants that probe the role in iron release of the dilysine pair in the N-lobe of human transferrin.
Authors: Baker, H.M. / Nurizzo, D. / Mason, A.B. / Baker, E.N.
History
DepositionDec 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3704
Polymers37,2151
Non-polymers1553
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.173, 57.317, 135.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 37215.203 Da / Num. of mol.: 1 / Fragment: N-lobe / Mutation: K206E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pNUT / Cell line (production host): BHK / Organ (production host): kidney / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P02787
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Protein: 35mg/ml, 0.1M ammonium bicrbonate. Well: 18% PEG3350, 0.2M potassium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 7, 2005 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→22.7 Å / Num. all: 10917 / Num. obs: 10917 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 32.58 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 9
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3 / Num. unique all: 1576 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.3.0008refinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: N-lobe human transferrin, PDB code 1A8E

1a8e


Resolution: 2.6→21.02 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.825 / SU B: 11.456 / SU ML: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 521 4.8 %RANDOM
Rwork0.213 ---
all0.216 10358 --
obs0.216 10358 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.6→21.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2551 0 6 129 2686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222623
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.9613552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3925328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63324.454119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2615435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7081512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022016
X-RAY DIFFRACTIONr_nbd_refined0.2050.21250
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21757
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2131
X-RAY DIFFRACTIONr_metal_ion_refined0.0450.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.29
X-RAY DIFFRACTIONr_mcbond_it0.461.51641
X-RAY DIFFRACTIONr_mcangle_it0.86822620
X-RAY DIFFRACTIONr_scbond_it1.2573996
X-RAY DIFFRACTIONr_scangle_it2.1164.5932
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 30 -
Rwork0.18 731 -
obs-761 100 %

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