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Open data
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Basic information
Entry | Database: PDB / ID: 1dsn | ||||||
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Title | D60S N-TERMINAL LOBE HUMAN LACTOFERRIN | ||||||
![]() | LACTOFERRIN | ||||||
![]() | IRON TRANSPORT PROTEIN / IRON TRANSPORT / GLYCOPROTEIN / METAL-BINDING | ||||||
Function / homology | ![]() 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 cysteine-type endopeptidase activity / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism ...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 cysteine-type endopeptidase activity / 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 lipopolysaccharide-mediated signaling pathway / negative regulation of osteoclast development / specific granule / antifungal humoral response / positive regulation of chondrocyte proliferation / negative regulation of ATP-dependent activity / regulation of tumor necrosis factor production / bone morphogenesis / Antimicrobial peptides / cysteine-type endopeptidase inhibitor activity / 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 osteoblast differentiation / regulation of cytokine production / protein serine/threonine kinase activator activity / ossification / innate immune response in mucosa / secretory granule / lipopolysaccharide binding / positive regulation of protein serine/threonine kinase activity / recycling endosome / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / positive regulation of NF-kappaB transcription factor activity / heparin binding / iron ion transport / antibacterial humoral response / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / killing of cells of another organism / 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 | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Faber, H.R. / Norris, G.E. / Baker, E.N. | ||||||
![]() | ![]() Title: Altered domain closure and iron binding in transferrins: the crystal structure of the Asp60Ser mutant of the amino-terminal half-molecule of human lactoferrin. Authors: Faber, H.R. / Bland, T. / Day, C.L. / Norris, G.E. / Tweedie, J.W. / Baker, E.N. #1: ![]() Title: Structure of the Recombinant N-Terminal Lobe of Human Lactoferrin at 2.0 Angstroms Resolution Authors: Day, C.L. / Anderson, B.F. / Tweedie, J.W. / Baker, E.N. #2: ![]() Title: Studies of the N-Terminal Half of Human Lactoferrin Produced from Cloned Cdna Demonstrate that Interlobe Interactions Modulate Iron Release Authors: Day, C.L. / Stowell, K.M. / Baker, E.N. / Tweedie, J.W. | ||||||
History |
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Remark 700 | SHEET SHEET 2 STRAND 5 IS A SPLIT STRAND, GLU 226 - CYS 231 AND STRAND HIS 246 - PRO 251. STRAND ...SHEET SHEET 2 STRAND 5 IS A SPLIT STRAND, GLU 226 - CYS 231 AND STRAND HIS 246 - PRO 251. STRAND HIS 246 - PRO 251 IS PRESENTED AS SHEET 2A IN THE ENTRY. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.2 KB | Display | ![]() |
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PDB format | ![]() | 57 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 71 / 2: CIS PROLINE - PRO 142 | ||||||||
Components on special symmetry positions |
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Components
#1: Protein | Mass: 37093.164 Da / Num. of mol.: 1 / Fragment: N-TERMINAL LOBE RESIDUES 1 - 333 / Mutation: D60S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-CO3 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.87 % | ||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 46 % | ||||||||||||||||||||
Crystal grow | *PLUS Method: microdialysis | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient temp details: ROOM |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IIC / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Redundancy: 2.8 % / Rmerge(I) obs: 0.052 |
Reflection | *PLUS Highest resolution: 2.05 Å / Num. obs: 17803 / % possible obs: 83.6 % / Observed criterion σ(I): 1 / Num. measured all: 49951 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS Highest resolution: 2.05 Å / Lowest resolution: 2.2 Å / % possible obs: 70.6 % / Mean I/σ(I) obs: 3.1 |
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Processing
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Refinement | Resolution: 2.05→20 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32.6 Å2 | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.013 |