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Yorodumi- PDB-1fy1: [R23S,F25E]HBP, A MUTANT OF HUMAN HEPARIN BINDING PROTEIN (CAP37) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fy1 | |||||||||
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Title | [R23S,F25E]HBP, A MUTANT OF HUMAN HEPARIN BINDING PROTEIN (CAP37) | |||||||||
Components | HEPARIN-BINDING PROTEIN | |||||||||
Keywords | ANTIMICROBIAL PROTEIN / Serine protease homolog / Endotoxin (lipid A) binding site | |||||||||
Function / homology | Function and homology information monocyte activation / neutrophil-mediated killing of bacterium / cellular extravasation / monocyte extravasation / positive regulation of fractalkine production / protein kinase C signaling / glial cell migration / regulation of vascular permeability / induction of positive chemotaxis / : ...monocyte activation / neutrophil-mediated killing of bacterium / cellular extravasation / monocyte extravasation / positive regulation of fractalkine production / protein kinase C signaling / glial cell migration / regulation of vascular permeability / induction of positive chemotaxis / : / positive regulation of MHC class II biosynthetic process / antimicrobial humoral response / heparan sulfate proteoglycan binding / azurophil granule / azurophil granule membrane / macrophage chemotaxis / positive regulation of cell adhesion / toxic substance binding / positive regulation of protein kinase activity / positive regulation of phagocytosis / cell chemotaxis / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-1 beta production / microglial cell activation / azurophil granule lumen / positive regulation of tumor necrosis factor production / heparin binding / peptidase activity / defense response to virus / defense response to Gram-negative bacterium / inflammatory response / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | |||||||||
Authors | Kastrup, J.S. / Linde, V. / Pedersen, A.K. / Stoffer, B. / Iversen, L.F. / Larsen, I.K. / Rasmussen, P.B. / Flodgaard, H.J. / Bjorn, S.E. | |||||||||
Citation | Journal: Proteins / Year: 2001 Title: Two mutants of human heparin binding protein (CAP37): toward the understanding of the nature of lipid A/LPS and BPTI binding. Authors: Kastrup, J.S. / Linde, V. / Pedersen, A.K. / Stoffer, B. / Iversen, L.F. / Larsen, I.K. / Rasmussen, P.B. / Flodgaard, H.J. / Bjorn, S.E. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Atomic resolution structure of human HBP/CAP37/Azurocidin Authors: Karlsen, S. / Iversen, L.F. / Larsen, I.K. / Flodgaard, H.J. / Kastrup, J.S. #2: Journal: Nat.Struct.Biol. / Year: 1997 Title: Structure of HBP, a multifunctional protein with a serine proteinase fold Authors: Iversen, L.F. / Kastrup, J.S. / Bjorn, S.E. / Rasmussen, P.B. / Wiberg, F.C. / Flodgaard, H.J. / Larsen, I.K. #3: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Crystallization and Molecular Replacement Solution of Human Heparin Binding Protein Authors: Iversen, L.F. / Kastrup, J.S. / Larsen, I.K. / Bjorn, S.E. / Rasmussen, P.B. / Wiberg, F.C. / Flodgaard, H.J. #4: Journal: Protein Sci. / Year: 1999 Title: Structure and function of the N-linked glycans of HBP/CAP37/azurocidin: Crystal structure determination and biological characterization of nonglycosylated HBP Authors: Iversen, L.F. / Kastrup, J.S. / Bjorn, S.E. / Wiberg, F.C. / Larsen, I.K. / Flodgaard, H.J. / Rasmussen, P.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fy1.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fy1.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 1fy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fy1_validation.pdf.gz | 712.2 KB | Display | wwPDB validaton report |
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Full document | 1fy1_full_validation.pdf.gz | 723.1 KB | Display | |
Data in XML | 1fy1_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 1fy1_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/1fy1 ftp://data.pdbj.org/pub/pdb/validation_reports/fy/1fy1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological unit is a monomer |
-Components
#1: Protein | Mass: 24214.299 Da / Num. of mol.: 1 / Mutation: R23S, F25E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF-900 / Production host: unidentified baculovirus / Strain (production host): ACMNPV / References: UniProt: P20160 | ||||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Sugar | #4: Chemical | ChemComp-EOH / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.09 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Ethanol, 1,2,5-trihydroxyhexane, TRIS, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.835 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.835 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 9554 / Num. obs: 9554 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 49.7 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.33 / Num. unique all: 463 / % possible all: 99.4 |
Reflection | *PLUS Num. measured all: 32904 |
Reflection shell | *PLUS % possible obs: 99.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.9 |
-Processing
Software |
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Refinement | Resolution: 2.5→20 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: TNT PROTGEO
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 1 / Rfactor obs: 0.207 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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