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- PDB-1hse: H253M N TERMINAL LOBE OF HUMAN LACTOFERRIN -

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Basic information

Entry
Database: PDB / ID: 1hse
TitleH253M N TERMINAL LOBE OF HUMAN LACTOFERRIN
ComponentsLACTOFERRIN
KeywordsIRON TRANSPORT / GLYCOPROTEIN / METAL-BINDING / DUPLICATION / MILK / RECOMBINANT HALF MOLECULE / TRANSFERRIN
Function / homology
Function and homology information


membrane destabilizing activity / host-mediated suppression of viral proces / Mtb iron assimilation by chelation / phagocytic vesicle lumen / Metal sequestration by antimicrobial proteins / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of viral process / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation ...membrane destabilizing activity / host-mediated suppression of viral proces / Mtb iron assimilation by chelation / phagocytic vesicle lumen / Metal sequestration by antimicrobial proteins / positive regulation of toll-like receptor 4 signaling pathway / negative regulation of viral process / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of osteoclast development / antifungal humoral response / specific granule / negative regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of chondrocyte proliferation / negative regulation of ATP-dependent activity / regulation of tumor necrosis factor production / bone morphogenesis / Antimicrobial peptides / negative regulation of viral genome replication / positive regulation of osteoblast proliferation / humoral immune response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of protein serine/threonine kinase activity / cysteine-type endopeptidase inhibitor activity / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / secretory granule / protein serine/threonine kinase activator activity / innate immune response in mucosa / lipopolysaccharide binding / iron ion transport / positive regulation of NF-kappaB transcription factor activity / recycling endosome / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / tertiary granule lumen / heparin binding / defense response to Gram-negative bacterium / killing of cells of another organism / early endosome / positive regulation of canonical NF-kappaB signal transduction / iron ion binding / Amyloid fiber formation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / protein-containing complex / proteolysis / extracellular space / DNA binding / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Lactotransferrin / 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 ...Lactotransferrin / 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
CARBONATE ION / : / Lactotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsNicholson, H. / Anderson, B.F. / Baker, E.N.
Citation
Journal: Biochemistry / Year: 1997
Title: Mutagenesis of the histidine ligand in human lactoferrin: iron binding properties and crystal structure of the histidine-253-->methionine mutant.
Authors: Nicholson, H. / Anderson, B.F. / Bland, T. / Shewry, S.C. / Tweedie, J.W. / Baker, E.N.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Structure of the Recombinant N-Terminal Lobe of Human Lactoferrin at 2.0 A Resolution
Authors: Day, C.L. / Anderson, B.F. / Tweedie, J.W. / Baker, E.N.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: Studies of the N-Terminal Half of Human Lactoferrin Produced from the Cloned Cdna Demonstrate that Interlobe Interactions Modulate Iron Release
Authors: Day, C.L. / Stowell, K.M. / Baker, E.N. / Tweedie, J.W.
History
DepositionDec 11, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LACTOFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3173
Polymers37,2011
Non-polymers1162
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.400, 58.400, 217.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein LACTOFERRIN / H253M NLF


Mass: 37201.305 Da / Num. of mol.: 1 / Fragment: N-TERMINAL HALF-MOLECULE / Mutation: H253M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: 293 / Gene: LFN / Plasmid: PNUT;LFN / Gene (production host): LFN / Production host: Cricetinae (hamsters) / Strain (production host): 293 / References: UniProt: P02788
#2: Chemical ChemComp-FE / FE (III) ION


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


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46 %
Crystal grow
*PLUS
pH: 8 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.01 MTris-HCl11
212 %(v/v)2-propanol11

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 14575 / % possible obs: 72 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.066
Reflection
*PLUS
Highest resolution: 2.2 Å

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Processing

Software
NameClassification
RIGAKUdata collection
TNTrefinement
RIGAKUdata reduction
RefinementResolution: 2.2→20 Å / σ(F): 0
Details: DIHEDRAL ANGLES. SER 191 IS IN THE EPSILON REGION. THIS RESIDUE HAS EXCELLENT DENSITY AND ITS PHI/PSI ANGLES ARE CORRECT. SER 293 HAS GOOD DENSITY, AND NO OTHER INTERPRETATION SEEMS POSSIBLE. ...Details: DIHEDRAL ANGLES. SER 191 IS IN THE EPSILON REGION. THIS RESIDUE HAS EXCELLENT DENSITY AND ITS PHI/PSI ANGLES ARE CORRECT. SER 293 HAS GOOD DENSITY, AND NO OTHER INTERPRETATION SEEMS POSSIBLE. ILE 299 IS THE CENTRAL RESIDUE OF A GAMMA TURN, AND HAS THE EXPECTED PHI/PSI ANGLES FOR SUCH A CONFORMATION. THIS CONFORMATION IS CONSERVED IN ALL TRANSFERRINS AND THE ELECTRON DENSITY IS EXCELLENT.
RfactorNum. reflection% reflection
Rwork0.178 --
obs-14537 72 %
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 5 113 2592
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0152
X-RAY DIFFRACTIONt_angle_deg1.881.3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.0152
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.015 / Weight: 2

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