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- PDB-1blf: STRUCTURE OF DIFERRIC BOVINE LACTOFERRIN AT 2.8 ANGSTROMS RESOLUTION -
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Open data
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Basic information
Entry | Database: PDB / ID: 1blf | |||||||||
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Title | STRUCTURE OF DIFERRIC BOVINE LACTOFERRIN AT 2.8 ANGSTROMS RESOLUTION | |||||||||
![]() | LACTOFERRIN | |||||||||
![]() | IRON-BINDING PROTEIN / LACTOFERRIN / TRANSFERRIN / CARBOHYDRATE STRUCTURE | |||||||||
Function / homology | ![]() Metal sequestration by antimicrobial proteins / Antimicrobial peptides / 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 ...Metal sequestration by antimicrobial proteins / Antimicrobial peptides / 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 / regulation of tumor necrosis factor production / bone morphogenesis / Neutrophil degranulation / cysteine-type endopeptidase inhibitor activity / positive regulation of osteoblast proliferation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / innate immune response in mucosa / recycling endosome / iron ion transport / antibacterial humoral response / early endosome / iron ion binding / serine-type endopeptidase activity / signaling receptor binding / negative regulation of apoptotic process / proteolysis / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Moore, S.A. / Anderson, B.F. / Groom, C.R. / Haridas, M. / Baker, E.N. | |||||||||
![]() | ![]() Title: Three-dimensional structure of diferric bovine lactoferrin at 2.8 A resolution. Authors: Moore, S.A. / Anderson, B.F. / Groom, C.R. / Haridas, M. / 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 | ![]() | 149.4 KB | Display | ![]() |
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PDB format | ![]() | 117 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 36.8 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 76244.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 3 types, 3 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 54 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CO3.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: USED SEPARATE N AND C LOBES | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: dialaysis / pH: 7.7 Details: 25 MM TRIS/HCL, PH 7.7 8% (V/V) MPD 6.5% (V/V) ETHANOL DIALYSED AGAINST A 200 MG/ML SOLUTION OF PROTEIN AT 277 K., dialaysis | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: microdialysis | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 1, 1994 / Details: 0.3 MM COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 22017 / % possible obs: 97 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 28 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4 / Rsym value: 0.31 / % possible all: 95.9 |
Reflection | *PLUS Num. measured all: 81067 |
Reflection shell | *PLUS % possible obs: 95.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: HUMAN LACTOFERRIN Resolution: 2.8→30 Å / Isotropic thermal model: BCORREL WITH MODIFICATIONS / Cross valid method: FREE R FACTOR / Stereochemistry target values: PROTGEO WITH MODIFICATIONS
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 150 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5EA / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.286 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 68.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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