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- PDB-1bp5: HUMAN SERUM TRANSFERRIN, RECOMBINANT N-TERMINAL LOBE, APO FORM -

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Basic information

Entry
Database: PDB / ID: 1bp5
TitleHUMAN SERUM TRANSFERRIN, RECOMBINANT N-TERMINAL LOBE, APO FORM
ComponentsPROTEIN (SERUM TRANSFERRIN)
KeywordsMETAL TRANSPORT / IRON TRANSPORT / GLYCOPROTEIN / TRANSFERRIN / NLOBE / IRON-RELEASE / CARBONATE
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 / clathrin-coated endocytic vesicle membrane / iron ion transport / Iron uptake and transport / ferrous iron binding / regulation of iron ion transport / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJeffrey, P.D. / Bewley, M.C. / Macgillivray, R.T.A. / Mason, A.B. / Woodworth, R.C. / Baker, E.N.
CitationJournal: Biochemistry / Year: 1998
Title: Ligand-induced conformational change in transferrins: crystal structure of the open form of the N-terminal half-molecule of human transferrin.
Authors: Jeffrey, P.D. / Bewley, M.C. / MacGillivray, R.T. / Mason, A.B. / Woodworth, R.C. / Baker, E.N.
History
DepositionAug 12, 1998Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 11, 2019Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.4Aug 9, 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX DETERMINATION METHOD: AUTHOR-DETERMINED HELIX_ID: 5,STARTS WITH TWO PI-TYPE H BONDS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (SERUM TRANSFERRIN)
B: PROTEIN (SERUM TRANSFERRIN)
C: PROTEIN (SERUM TRANSFERRIN)
D: PROTEIN (SERUM TRANSFERRIN)


Theoretical massNumber of molelcules
Total (without water)148,8614
Polymers148,8614
Non-polymers00
Water9,980554
1
A: PROTEIN (SERUM TRANSFERRIN)


Theoretical massNumber of molelcules
Total (without water)37,2151
Polymers37,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN (SERUM TRANSFERRIN)


Theoretical massNumber of molelcules
Total (without water)37,2151
Polymers37,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROTEIN (SERUM TRANSFERRIN)


Theoretical massNumber of molelcules
Total (without water)37,2151
Polymers37,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PROTEIN (SERUM TRANSFERRIN)


Theoretical massNumber of molelcules
Total (without water)37,2151
Polymers37,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.500, 77.300, 107.500
Angle α, β, γ (deg.)90.00, 98.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PROTEIN (SERUM TRANSFERRIN)


Mass: 37215.270 Da / Num. of mol.: 4 / Fragment: N-TERMINAL LOBE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: EXTRACELLULAR / Cell (production host): KIDNEY CELL / Organ (production host): KIDNEY / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P02787
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 46 %
Crystal growpH: 5.3
Details: PROTEIN WAS CRYSTALLIZED FROM 35% MPD. BUFFER WAS 50MM POTASSIUM ACETATE, PH 5.3, WITH 50MM KCL, AND 20MM NA BICARBONATE CRYSTALS GROWN AT 4 DEGREES C USING THE SITTING DROP METHOD.
Crystal
*PLUS
Density % sol: 46 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 mM1dropNaHCO3
350 mM1dropKCl
450 mMpotassium acetate1reservoir
535 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 15, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→37 Å / Num. obs: 73066 / % possible obs: 79.9 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 9.2
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 4 / % possible all: 61.1
Reflection shell
*PLUS
% possible obs: 61.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INDIVIDUAL DOMAINS OF HUMAN TRANSFERRIN N-TERMINAL HALF-MOLECULE (FE FORM) 1A8E

1a8e


Resolution: 2.2→6 Å / Isotropic thermal model: INDIVIDUAL ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.292 5860 10 %RANDOM
Rwork0.203 ---
obs0.203 58663 80 %-
Displacement parametersBiso mean: 40.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10256 0 0 554 10810
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 6 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.5 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.7

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