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- PDB-1lfg: Structure of diferric human lactoferrin -

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Entry
Database: PDB / ID: 1lfg
TitleStructure of diferric human lactoferrin
ComponentsLACTOFERRIN
KeywordsTRANSFERRIN
Function / homology
Function and homology information


host-mediated suppression of viral proces / membrane destabilizing activity / 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 ...host-mediated suppression of viral proces / membrane destabilizing activity / 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 / Amyloid fiber formation / iron ion binding / 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
AuthorsBaker, E.N. / Anderson, B.F. / Haridas, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of human diferric lactoferrin refined at 2.2 A resolution.
Authors: Haridas, M. / Anderson, B.F. / Baker, E.N.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Structure of Human Lactoferrin: Crystallographic Structure Analysis and Refinement at 2.8 Angstroms Resolution
Authors: Anderson, B.F. / Baker, H.M. / Norris, G.E. / Rice, D.W. / Baker, E.N.
#2: Journal: Trends Biochem.Sci.(Pers. Ed.) / Year: 1987
Title: Transferrins: Insights Into Structure and Function from Studies on Lactoferrin
Authors: Baker, E.N. / Rumball, S.V. / Anderson, B.F.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Structure of Human Lactoferrin at 3.2 Angstroms Resolution
Authors: Anderson, B.F. / Baker, H.M. / Dodson, E.J. / Norris, G.E. / Rumball, S.V. / Waters, J.M. / Baker, E.N.
History
DepositionFeb 5, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 1, 2012Group: Database references / Structure summary
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_sheet / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_sheet.number_strands / _struct_site_gen.auth_seq_id
Remark 700SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS ...SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS *N2A* AND *N2B* REPRESENT ONE BIFURCATED SHEET WHERE STRAND 4 OF SHEET RECORD BN1 IS ALSO PART OF THIS SHEET. SHEETS *C2A* AND *C2B* REPRESENT ONE BIFURCATED SHEET WHERE STRAND 4 OF SHEET RECORD BC1 IS ALSO PART OF THIS SHEET.
Remark 650HELIX ON HELIX RECORDS THE TYPES OF DISTORTION IN H BONDING OF N AND C TERMINI CLASSIFIED AS IN F.N. ...HELIX ON HELIX RECORDS THE TYPES OF DISTORTION IN H BONDING OF N AND C TERMINI CLASSIFIED AS IN F.N.BAKER AND R.F.HUBBARD (1984) PROG. BIOPHYS. MOL. BIOL. 44, 97-179.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LACTOFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2497
Polymers76,0791
Non-polymers1,1706
Water8,881493
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.260, 97.400, 55.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 71 / 2: CIS PROLINE - PRO 142 / 3: CIS PROLINE - PRO 628 / 4: RESIDUES 1-4 POORLY DEFINED DENSITY. / 5: RESIDUES 293-294 POORLY DEFINED DENSITY. / 6: RESIDUES 418-422 POORLY DEFINED DENSITY. / 7: ASN 137 CARBOHYDRATE ATTACHMENT SITE. / 8: ASN 478 CARBOHYDRATE ATTACHMENT SITE.
9: NO SIDECHAINS BEYOND CB FOR ARG 86 AND GLU 637 (TREATED AS ALA).

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LACTOFERRIN


Mass: 76079.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P02788

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 497 molecules

#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTWO-FOLD INTERNAL SEQUENCE HOMOLOGY (~ 40% IDENTITY). ONE BINDING SITE IN EACH LOBE.
Has protein modificationY
Nonpolymer detailsVERY POOR DENSITY FOR THE CARBOHYDRATE - NOT ACCURATELY MODELLED.
Sequence detailsAMINO ACID SEQUENCE GIVEN IN ANDERSON ET AL. (1989) (COMPOSITE OF CHEMICALLY-DETERMINED AND CDNA ...AMINO ACID SEQUENCE GIVEN IN ANDERSON ET AL. (1989) (COMPOSITE OF CHEMICALLY-DETERMINED AND CDNA SEQUENCES). SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: TRFL_HUMAN SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLN 13 ASN 13 THR 43 ILE 43 ARG 200 LYS 200 CYS 403 GLY 403 GLN 418 ALA 418 ARG 500 ALA 500 GLU 512 GLN 512

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.8 / Method: microdialysis
Details: taken from Baker, E.N. et al (1977). J. Mol. Biol., 111, 207-210.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-5 %protein11
20.01 Mphosphate12
310 %(v/v)ethanol12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 17783 / Rmerge(I) obs: 0.09

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementRfactor obs: 0.183 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5322 0 71 493 5886
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 0.055

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