+Open data
-Basic information
Entry | Database: PDB / ID: 1ae5 | ||||||
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Title | HUMAN HEPARIN BINDING PROTEIN | ||||||
Components | HEPARIN BINDING PROTEIN | ||||||
Keywords | SERINE PROTEASE HOMOLOG / ENDOTOXIN BINDING / HEPARIN BINDING / INFLAMMATION / ANTIBACTERIAL / CAP37 / AZUROCIDIN / GLYCOSYLATED PROTEIN | ||||||
Function / homology | Function and homology information monocyte activation / neutrophil-mediated killing of bacterium / cellular 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 ...monocyte activation / neutrophil-mediated killing of bacterium / cellular 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 / positive regulation of tumor necrosis factor production / azurophil granule lumen / peptidase activity / heparin binding / defense response to Gram-negative bacterium / defense response to virus / inflammatory response / intracellular membrane-bounded organelle / serine-type endopeptidase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Iversen, L.F. / Kastrup, J.S. / Bjorn, S.E. / Rasmussen, P.B. / Wiberg, F.C. / Flodgaard, H.J. / Larsen, I.K. | ||||||
Citation | 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. #1: 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. #2: Journal: FEBS Lett. / Year: 1996 Title: Characterization of Recombinant Human Hbp/CAP37/Azurocidin, a Pleiotropic Mediator of Inflammation-Enhancing Lps-Induced Cytokine Release from Monocytes Authors: Rasmussen, P.B. / Bjorn, S. / Hastrup, S. / Nielsen, P.F. / Norris, K. / Thim, L. / Wiberg, F.C. / Flodgaard, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ae5.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ae5.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ae5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ae5_validation.pdf.gz | 413.4 KB | Display | wwPDB validaton report |
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Full document | 1ae5_full_validation.pdf.gz | 422.2 KB | Display | |
Data in XML | 1ae5_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 1ae5_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/1ae5 ftp://data.pdbj.org/pub/pdb/validation_reports/ae/1ae5 | HTTPS FTP |
-Related structure data
Related structure data | 1ppfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24302.475 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: SF-900 / Cell line (production host): SF-900 / Production host: unidentified baculovirus / Strain (production host): ACMNPV / References: UniProt: P20160 | ||
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#2: Sugar | #3: 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: 2.3 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.2 / Details: pH 7.2 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Iversen, L.F., (1996) Acta Crystallogr.,Sect.D, 52, 1222. | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.999 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 12176 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.264 / % possible all: 98.6 |
Reflection shell | *PLUS % possible obs: 98.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PPF Resolution: 2.3→20 Å / σ(F): 1 Details: THERE IS A DISORDERED REGION IN THE STRUCTURE INVOLVING RESIDUES 44 - 48.
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.192 / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.192 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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