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- PDB-1lct: STRUCTURE OF THE RECOMBINANT N-TERMINAL LOBE OF HUMAN LACTOFERRIN... -

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Entry
Database: PDB / ID: 1lct
TitleSTRUCTURE OF THE RECOMBINANT N-TERMINAL LOBE OF HUMAN LACTOFERRIN AT 2.0 ANGSTROMS RESOLUTION
ComponentsLACTOFERRIN
KeywordsIRON TRANSPORT
Function / homology
Function and homology information


negative regulation by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / 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 by host of viral process / membrane destabilizing activity / Mtb iron assimilation by chelation / phagocytic vesicle lumen / positive regulation of toll-like receptor 4 signaling pathway / Metal sequestration by antimicrobial proteins / 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 / cysteine-type endopeptidase inhibitor activity / positive regulation of protein serine/threonine kinase activity / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / innate immune response in mucosa / protein serine/threonine kinase activator activity / secretory granule / lipopolysaccharide binding / recycling endosome / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of NF-kappaB transcription factor activity / antibacterial humoral response / tertiary granule lumen / heparin binding / iron ion transport / defense response to Gram-negative bacterium / killing of cells of another organism / positive regulation of canonical NF-kappaB signal transduction / early endosome / iron ion binding / Amyloid fiber formation / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / protein-containing complex / proteolysis / DNA binding / extracellular space / 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 Å
AuthorsDay, C.L. / Anderson, B.F. / Baker, E.N.
Citation
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.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Preliminary Crystallographic Studies of the Amino-Terminal Half of Human Lactoferrin in its Iron-Saturated and Iron-Free Forms
Authors: Day, C.L. / Norris, G.E. / Anderson, B.F. / Tweedie, J.W. / Baker, E.N.
#3: 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.
History
DepositionJun 19, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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
Remark 700SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 1, 2, 3, 4 AND 6 OF B2A AND B2B ARE IDENTICAL.

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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)37,1953
Polymers37,0791
Non-polymers1162
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.000, 58.300, 58.300
Angle α, β, γ (deg.)90.00, 114.70, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: THERE WAS NO SIDE CHAIN DENSITY FOR RESIDUES 4, 38, 73, 85, 86, 137, 139, AND 315. ALL WERE TREATED AS ALA DURING REFINEMENT.
2: RESIDUES 71 AND 142 ARE CIS PROLINES.

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Components

#1: Protein LACTOFERRIN


Mass: 37079.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDNA / 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.: 186 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PROTEIN WAS DEGLYCOSYLATED PRIOR TO CRYSTALLIZATION.
Has protein modificationY
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...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 129 ILE 129 THE SEQUENCE DEVIATIONS RESULT FROM THE AUTHOR'S OWN SEQUENCING OF A CDNA FOR HUMAN LACTOFERRIN. THE SEQUENCE USED IN THE STRUCTURAL WORK IS THAT GIVEN IN THE PAPER PRESENTED AS REFERENCE 3 ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.8 / Method: microdialysis
Details: taken from Day, C.L. et al(1992). J. Mol. Biol., 228, 973-974.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.1 M11NaHCO3
20.2 M11NaCl
30.01 MHEPES11
4ethanol11or 12 % isopropanol

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. all: 111279 / Num. obs: 35000 / Rmerge(I) obs: 0.075

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2→8 Å / σ(F): 0 /
RfactorNum. reflection
obs0.184 34180
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 5 186 2680
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg3
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_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. reflection all: 34180 / σ(F): 0 / Rfactor all: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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