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Open data
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Basic information
Entry | Database: PDB / ID: 1bka | ||||||
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Title | OXALATE-SUBSTITUTED DIFERRIC LACTOFERRIN | ||||||
![]() | LACTOFERRIN | ||||||
![]() | IRON BINDING PROTEIN / ANION BINDING | ||||||
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 | ![]() ![]() | ||||||
![]() | Baker, H.M. / Smith, C.A. / Baker, E.N. | ||||||
![]() | ![]() Title: Anion binding by transferrins: importance of second-shell effects revealed by the crystal structure of oxalate-substituted diferric lactoferrin. Authors: Baker, H.M. / Anderson, B.F. / Brodie, A.M. / Shongwe, M.S. / Smith, C.A. / Baker, E.N. #1: ![]() Title: Structure of Human Diferric Lactoferrin Refined at 2.2 Angstroms Resolution Authors: Haridas, M. / Anderson, B.F. / Baker, E.N. #2: ![]() 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. #3: ![]() Title: Structure of Human Lactoferrin: Crystallographic Structure Analysis and Refinement at 2.8 A Resolution Authors: Anderson, B.F. / Baker, H.M. / Norris, G.E. / Rice, D.W. / Baker, E.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 152.9 KB | Display | ![]() |
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PDB format | ![]() | 115.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.1 KB | Display | ![]() |
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Full document | ![]() | 497.3 KB | Display | |
Data in XML | ![]() | 26.8 KB | Display | |
Data in CIF | ![]() | 37.5 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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Unit cell |
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Components
#1: Protein | Mass: 76263.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: microdialysis | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 15, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Num. obs: 31874 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.115 |
Reflection | *PLUS Highest resolution: 2.4 Å |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.54 Å / % possible obs: 83.3 % |
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Processing
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Refinement | Resolution: 2.4→8 Å / Num. reflection obs: 31758 / σ(F): 0 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.196 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |