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Yorodumi- PDB-1lct: STRUCTURE OF THE RECOMBINANT N-TERMINAL LOBE OF HUMAN LACTOFERRIN... -
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-Basic information
Entry | Database: PDB / ID: 1lct | ||||||
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Title | STRUCTURE OF THE RECOMBINANT N-TERMINAL LOBE OF HUMAN LACTOFERRIN AT 2.0 ANGSTROMS RESOLUTION | ||||||
Components | LACTOFERRIN | ||||||
Keywords | IRON 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 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 / negative regulation of ATP-dependent activity / positive regulation of chondrocyte proliferation / 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 / heparin binding / positive regulation of NF-kappaB transcription factor activity / antibacterial humoral response / iron ion transport / positive regulation of canonical NF-kappaB signal transduction / killing of cells of another organism / defense response to Gram-negative bacterium / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Day, 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 |
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Remark 700 | SHEET 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lct.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lct.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 1lct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/1lct ftp://data.pdbj.org/pub/pdb/validation_reports/lc/1lct | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: 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. |
-Components
#1: Protein | 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 | ||
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#2: Chemical | ChemComp-FE / | ||
#3: Chemical | ChemComp-CO3 / | ||
#4: Water | ChemComp-HOH / | ||
Compound details | THE PROTEIN WAS DEGLYCOSYLSequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.55 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.8 / Method: microdialysisDetails: taken from Day, C.L. et al(1992). J. Mol. Biol., 228, 973-974. | |||||||||||||||||||||||||||||||||||
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: 1.8 Å / Num. all: 111279 / Num. obs: 35000 / Rmerge(I) obs: 0.075 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→8 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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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
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