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Yorodumi- PDB-6san: SALSA / DMBT1 / GP340 SRCR domain 8 soaked in calcium and magnesium -
+Open data
-Basic information
Entry | Database: PDB / ID: 6san | |||||||||
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Title | SALSA / DMBT1 / GP340 SRCR domain 8 soaked in calcium and magnesium | |||||||||
Components | Deleted in malignant brain tumors 1 protein | |||||||||
Keywords | IMMUNE SYSTEM / Scavenger receptor cysteine-rich / pattern recognition / mucosal immunology / anti-microbial molecule / complement / innate immunity / inflammation / salivary agglutinin / salivary scavenger and agglutinin / metal binding / calcium dependency | |||||||||
Function / homology | Function and homology information induction of bacterial agglutination / zymogen granule membrane / scavenger receptor activity / Surfactant metabolism / zymogen binding / pattern recognition receptor activity / epithelial cell differentiation / extracellular matrix / defense response / phagocytic vesicle membrane ...induction of bacterial agglutination / zymogen granule membrane / scavenger receptor activity / Surfactant metabolism / zymogen binding / pattern recognition receptor activity / epithelial cell differentiation / extracellular matrix / defense response / phagocytic vesicle membrane / calcium-dependent protein binding / protein transport / defense response to Gram-negative bacterium / defense response to virus / defense response to Gram-positive bacterium / innate immune response / extracellular space / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | |||||||||
Authors | Reichhardt, M.P. / Johnson, S. / Loimaranta, V. / Lea, S.M. | |||||||||
Funding support | Finland, United Kingdom, 2items
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Citation | Journal: Life Sci Alliance / Year: 2020 Title: Structures of SALSA/DMBT1 SRCR domains reveal the conserved ligand-binding mechanism of the ancient SRCR fold. Authors: Reichhardt, M.P. / Loimaranta, V. / Lea, S.M. / Johnson, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6san.cif.gz | 171.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6san.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 6san.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6san_validation.pdf.gz | 3.6 MB | Display | wwPDB validaton report |
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Full document | 6san_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 6san_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 6san_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/6san ftp://data.pdbj.org/pub/pdb/validation_reports/sa/6san | HTTPS FTP |
-Related structure data
Related structure data | 6sa4C 6sa5SC S: Starting model for refinement C: citing same article (ref.) |
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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: 14669.384 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DMBT1, GP340 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9UGM3 #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.39 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 50 % of 0.2 M MgCl2 hexahydrate, 20 % (v/v) isopropanol, 0.1 M HEPES, pH: 7.5. After crystal-formation, crystals were soaked in 10 mM MgCl2 and 10 mM CaCl2. |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→46.64 Å / Num. obs: 49168 / % possible obs: 98.32 % / Redundancy: 6.6 % / Biso Wilson estimate: 14.12 Å2 / Rrim(I) all: 0.074 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.36→1.39 Å / Num. unique obs: 4786 / Rrim(I) all: 0.801 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6sa5 Resolution: 1.36→30.95 Å / SU ML: 0.1911 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.6788 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→30.95 Å
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Refine LS restraints |
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LS refinement shell |
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