+Open data
-Basic information
Entry | Database: PDB / ID: 1a7s | |||||||||
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Title | ATOMIC RESOLUTION STRUCTURE OF HBP | |||||||||
Components | HEPARIN BINDING PROTEIN | |||||||||
Keywords | SERINE PROTEASE HOMOLOG / ENDOTOXIN BINDING / HEPARIN | |||||||||
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 / PHASES FROM NATIVE HBP / Resolution: 1.12 Å | |||||||||
Authors | Karlsen, S. / Iversen, L.F. / Larsen, I.K. / Flodgaard, H.J. / Kastrup, J.S. | |||||||||
Citation | 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. #1: 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. #2: 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a7s.cif.gz | 112.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a7s.ent.gz | 88.5 KB | Display | PDB format |
PDBx/mmJSON format | 1a7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a7s_validation.pdf.gz | 801.3 KB | Display | wwPDB validaton report |
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Full document | 1a7s_full_validation.pdf.gz | 806.8 KB | Display | |
Data in XML | 1a7s_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 1a7s_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/1a7s ftp://data.pdbj.org/pub/pdb/validation_reports/a7/1a7s | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24302.475 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: ACMNPV / Cell line (production host): SF-900 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P20160 |
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-Sugars , 2 types, 2 molecules
#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 |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 339 molecules
#4: Chemical | ChemComp-CL / | ||
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#5: Chemical | ChemComp-EOH / #6: 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 drop / Details: used microseeding | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / 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: 1.12→20 Å / Num. obs: 90539 / % possible obs: 90.5 % / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 7.13 |
Reflection shell | Resolution: 1.12→1.14 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 1.96 / % possible all: 81.9 |
Reflection shell | *PLUS % possible obs: 81.9 % / Num. unique obs: 4055 |
-Processing
Software |
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Refinement | Method to determine structure: PHASES FROM NATIVE HBP / Resolution: 1.12→15 Å / Num. parameters: 18822 / Num. restraintsaints: 85714 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 1626 / Occupancy sum non hydrogen: 2083 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→15 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-96 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.159 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |