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- PDB-1lfh: MOLECULAR REPLACEMENT SOLUTION OF THE STRUCTURE OF APOLACTOFERRIN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lfh | ||||||
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Title | MOLECULAR REPLACEMENT SOLUTION OF THE STRUCTURE OF APOLACTOFERRIN, A PROTEIN DISPLAYING LARGE-SCALE CONFORMATIONAL CHANGE | ||||||
![]() | LACTOFERRIN | ||||||
![]() | IRON TRANSPORT | ||||||
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 / specific granule / negative regulation of osteoclast development / 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 | ![]() | ||||||
![]() | Anderson, B.F. / Baker, E.N. / Norris, G.E. | ||||||
![]() | ![]() Title: Molecular replacement solution of the structure of apolactoferrin, a protein displaying large-scale conformational change. Authors: Norris, G.E. / Anderson, B.F. / Baker, E.N. #1: ![]() Title: Apolactoferrin Structure Demonstrates Ligand-Induced Conformational Change in Transferrins Authors: Anderson, B.F. / Baker, H.M. / Norris, G.E. / Rumball, S.V. / Baker, E.N. #2: ![]() 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. #3: ![]() Title: Transferrins: Insights Into Structure and Function from Studies on Lactoferrin Authors: Baker, E.N. / Rumball, S.V. / Anderson, B.F. #4: ![]() 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 |
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Remark 700 | SHEET 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 AND STRAND FOUR OF SHEET BN1 IS ALSO PART OF THIS SHEET. SHEETS *C2A* AND *C2B* REPRESENT ONE BIFURCATED SHEET AND STRAND FOUR OF SHEET BC1 IS ALSO PART OF THIS SHEET. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154 KB | Display | ![]() |
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PDB format | ![]() | 122.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.8 KB | Display | ![]() |
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Full document | ![]() | 485.3 KB | Display | |
Data in XML | ![]() | 37.7 KB | Display | |
Data in CIF | ![]() | 52.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 / 3: CIS PROLINE - PRO 628 |
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Components
#1: Protein | Mass: 76222.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Compound details | THERE IS A TWO FOLD INTERNAL SEQUENCE HOMOLOGY (~40% IDENTITY). |
Sequence details | THE AMINO ACID SEQUENCE GIVEN IN ANDERSON ET AL. (1989). WAS FOLLOWED IN BUILDING THE MODEL. THIS ...THE AMINO ACID SEQUENCE GIVEN IN ANDERSON ET AL. (1989). WAS FOLLOWED IN BUILDING THE MODEL. THIS PAPER REPORTS CORRECTION |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.25 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.8 / Method: microdialysisDetails: taken from Baker, E.N. et al (1977). J. Mol. Biol., 111, 207-210. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. obs: 17783 / Num. measured all: 19413 / Rmerge(I) obs: 0.09 |
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Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.213 / Highest resolution: 2.8 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 10 Å / Rfactor obs: 0.213 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |