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Yorodumi- PDB-1lfi: METAL SUBSTITUTION IN TRANSFERRINS: THE CRYSTAL STRUCTURE OF HUMA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lfi | |||||||||
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Title | METAL SUBSTITUTION IN TRANSFERRINS: THE CRYSTAL STRUCTURE OF HUMAN COPPER-LACTOFERRIN AT 2.1 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 / 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 / ossification / regulation of cytokine production / protein serine/threonine kinase activator activity / 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 / positive regulation of canonical NF-kappaB signal transduction / iron ion transport / antibacterial humoral response / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | |||||||||
Authors | Smith, C.A. / Anderson, B.F. / Baker, H.M. / Baker, E.N. | |||||||||
Citation | Journal: Biochemistry / Year: 1992 Title: Metal substitution in transferrins: the crystal structure of human copper-lactoferrin at 2.1-A resolution. Authors: Smith, C.A. / Anderson, B.F. / Baker, H.M. / Baker, E.N. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Preliminary Crystallographic Studies of Copper(II)-and Oxalate-Substituted Human Lactoferrin Authors: Smith, C.A. / Baker, H.M. / Baker, E.N. #2: 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. #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 |
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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. SHEETS *C2A* AND *C2B* REPRESENT ONE BIFURCATED SHEET AND STRAND 4 OF SHEET RECORD BC1 IS ALSO A PART OF THIS SHEET. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lfi.cif.gz | 156.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lfi.ent.gz | 120.6 KB | Display | PDB format |
PDBx/mmJSON format | 1lfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lfi_validation.pdf.gz | 527.6 KB | Display | wwPDB validaton report |
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Full document | 1lfi_full_validation.pdf.gz | 622.2 KB | Display | |
Data in XML | 1lfi_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 1lfi_validation.cif.gz | 41.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/1lfi ftp://data.pdbj.org/pub/pdb/validation_reports/lf/1lfi | HTTPS FTP |
-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: RESIDUES 1 - 4 ARE POORLY DEFINED IN THE DENSITY. / 2: RESIDUES ARG 2 AND ARG 3 WERE MODELLED AS ALA. / 3: RESIDUE LEU 37 WAS MODELLED AS ILE. / 4: CIS PROLINE - PRO 71 / 5: ASN 137 - CARBOHYDRATE ATTACHMENT SITE. / 6: CIS PROLINE - PRO 142 / 7: ASN 478 - CARBOHYDRATE ATTACHMENT SITE. / 8: RESIDUE GLN 418 WAS MODELLED AS ALA. / 9: RESIDUE ARG 500 WAS MODELLED AS ALA. / 10: CIS PROLINE - PRO 628 |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 76250.227 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 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 305 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | ONE COPPER(II) ION AND ONE CARBONATE ION ARE ASSOCIATED WITH EACH LOBE. TWO CARBOHYDRATE CHAINS ARE ...ONE COPPER(II) ION AND ONE CARBONATE ION ARE ASSOCIATED |
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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: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.68 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: microdialysisDetails: taken from Norris, G.E. et al (1989). J. Mol. Biol., 209, 329-331. PH range low: 8 / PH range high: 7.8 | ||||||||||||||||||||
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: 2.1 Å / Num. obs: 46683 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.4 Å / % possible obs: 33 % / Num. unique obs: 4081 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.199 / Highest resolution: 2.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.1 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 7.5 Å / Num. reflection obs: 43525 / σ(I): 0.5 / Rfactor obs: 0.199 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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