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Yorodumi- PDB-1lcf: CRYSTAL STRUCTURE OF COPPER-AND OXALATE-SUBSTITUTED HUMAN LACTOFE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lcf | ||||||
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Title | CRYSTAL STRUCTURE OF COPPER-AND OXALATE-SUBSTITUTED 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 / 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 Å | ||||||
Authors | Smith, C.A. / Anderson, B.F. / Baker, H.M. / Baker, E.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: Structure of copper- and oxalate-substituted human lactoferrin at 2.0 A resolution. Authors: Smith, C.A. / Anderson, B.F. / Baker, H.M. / Baker, E.N. #1: Journal: Biochemistry / Year: 1992 Title: Anion Binding by Human Lactoferrin: Results from Crystallographic and Physicochemical Studies Authors: Shongwe, M.S. / Smith, C.A. / Ainscough, E.W. / Baker, H.M. / Brodie, A.M. / Baker, E.N. #2: 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. #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 STRAND 4 OF SHEET *BN1* ON *SHEET* RECORDS BELOW ALSO APPEARS IN SHEET *BN2*. SHEET BN2 OF ...SHEET STRAND 4 OF SHEET *BN1* ON *SHEET* RECORDS BELOW ALSO APPEARS IN SHEET *BN2*. SHEET BN2 OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 1, 2, 3, AND 4 OF BN2 AND BN3 ARE IDENTICAL. STRAND 4 OF SHEET *BC1* ON *SHEET* RECORDS BELOW ALSO APPEARS IN SHEET *BC2*. SHEET BC2 OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 1, 2, 3, AND 4 OF BC2 AND BC3 ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lcf.cif.gz | 155.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lcf.ent.gz | 120.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lcf_validation.pdf.gz | 469.5 KB | Display | wwPDB validaton report |
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Full document | 1lcf_full_validation.pdf.gz | 553.9 KB | Display | |
Data in XML | 1lcf_validation.xml.gz | 41.7 KB | Display | |
Data in CIF | 1lcf_validation.cif.gz | 56.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/1lcf ftp://data.pdbj.org/pub/pdb/validation_reports/lc/1lcf | 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: CIS PROLINE - PRO 71 / 2: CIS PROLINE - PRO 142 / 3: CIS PROLINE - PRO 628 |
-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 76221.227 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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#2: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 329 molecules
#3: Chemical | #4: Chemical | ChemComp-CO3 / | #5: Chemical | ChemComp-OXL / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.87 % | ||||||||||||||||||||
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Crystal grow | *PLUS Method: microdialysis / 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 Å / Num. obs: 38143 / % possible obs: 75 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.077 / Biso Wilson estimate: 34 Å2 |
-Processing
Software | Name: PROFFT / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→8 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROFFT / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.193 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 41.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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