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- PDB-2bjj: Structure of recombinant human lactoferrin produced in the milk o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bjj | ||||||
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Title | Structure of recombinant human lactoferrin produced in the milk of transgenic cows | ||||||
![]() | LACTOTRANSFERRIN | ||||||
![]() | METAL BINDING PROTEIN / METAL-BINDING PROTEIN / LACTOFERRIN / TRANSGENIC COWS / IRON-BINDING / ANTIBIOTIC / GLYCOPROTEIN / POLYMORPHISM | ||||||
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 | ![]() ![]() | ||||||
![]() | Thomassen, E.A.J. / Van Veen, H.A. / Van Berkel, P.H.C. / Nuijens, J.H. / Abrahams, J.P. | ||||||
![]() | ![]() Title: The Protein Structure of Recombinant Human Lactoferrin Produced in the Milk of Transgenic Cows Closely Matches the Structure of Human Milk-Derived Lactoferrin Authors: Thomassen, E.A.J. / Van Veen, H.A. / Van Berkel, P.H.C. / Nuijens, J.H. / Abrahams, J.P. #1: Journal: Nat.Biotechnol. / Year: 2002 Title: Large Scale Production of Recombinant Human Lactoferrin in the Milk of Transgenic Cows Authors: Van Berkel, P.H.C. / Welling, M.M. / Geerts, M. / Van Veen, H.A. / Ravensbergen, B. / Salaheddine, M. / Pauwels, E.K.J. / Pieper, F. / Nuijens, J.N. / Nibbering, P.H. #2: ![]() Title: Structure of Human Diferric Lactoferrin Refined at 2.2 Angstrom Resolution Authors: Haridas, M. / Anderson, B.F. / Baker, E.N. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.4 KB | Display | ![]() |
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PDB format | ![]() | 116 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1lfgS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 76434.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | #4: Sugar | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.62 % |
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Crystal grow | pH: 8.5 / Details: 5 MM SODIUM PHOSPHATE PH 8.5, 10% (V/V) ETHANOL |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 29, 2003 / Details: OSMIC MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→81.65 Å / Num. obs: 33492 / % possible obs: 96.2 % / Observed criterion σ(I): 3.5 / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LFG Resolution: 2.4→19.63 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.083 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→19.63 Å
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Refine LS restraints |
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