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Yorodumi- PDB-1egi: STRUCTURE OF A C-TYPE CARBOHYDRATE-RECOGNITION DOMAIN (CRD-4) FRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1egi | ||||||
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Title | STRUCTURE OF A C-TYPE CARBOHYDRATE-RECOGNITION DOMAIN (CRD-4) FROM THE MACROPHAGE MANNOSE RECEPTOR | ||||||
Components | MACROPHAGE MANNOSE RECEPTOR | ||||||
Keywords | SUGAR BINDING PROTEIN / C-type lectin / mannose receptor | ||||||
Function / homology | Function and homology information cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / cellular response to interleukin-4 / receptor-mediated endocytosis / cellular response to type II interferon / transmembrane signaling receptor activity / Modulation by Mtb of host immune system / virus receptor activity / signaling receptor activity ...cargo receptor activity / Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / cellular response to interleukin-4 / receptor-mediated endocytosis / cellular response to type II interferon / transmembrane signaling receptor activity / Modulation by Mtb of host immune system / virus receptor activity / signaling receptor activity / cellular response to lipopolysaccharide / endosome membrane / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Feinberg, H. / Park-Snyder, S. / Kolatkar, A.R. / Heise, C.T. / Taylor, M.E. / Weis, W.I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Structure of a C-type carbohydrate recognition domain from the macrophage mannose receptor. Authors: Feinberg, H. / Park-Snyder, S. / Kolatkar, A.R. / Heise, C.T. / Taylor, M.E. / Weis, W.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1egi.cif.gz | 66.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1egi.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 1egi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1egi_validation.pdf.gz | 437.4 KB | Display | wwPDB validaton report |
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Full document | 1egi_full_validation.pdf.gz | 443.7 KB | Display | |
Data in XML | 1egi_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 1egi_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/1egi ftp://data.pdbj.org/pub/pdb/validation_reports/eg/1egi | HTTPS FTP |
-Related 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: 16800.596 Da / Num. of mol.: 2 / Fragment: CARBOHYDRATE-RECOGNITION DOMAIN 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P22897 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.04 Å3/Da / Density % sol: 39.59 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 8-13% polyethylene glycol, 100 mM Tris pH 8.0, 100 mM NaCl, 10 mM CaCl2, 100 mM a-Me-Man. The crystals were then transferred to a solution containing 200 mM methyl 3-O-(a-D-mannopyranosyl)-a- ...Details: 8-13% polyethylene glycol, 100 mM Tris pH 8.0, 100 mM NaCl, 10 mM CaCl2, 100 mM a-Me-Man. The crystals were then transferred to a solution containing 200 mM methyl 3-O-(a-D-mannopyranosyl)-a-D-mannopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 8, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. all: 12333 / Num. obs: 12246 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.064 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.354 / Num. unique all: 603 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 103297 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Resolution: 2.3→500 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 766262.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.12 Å2 / ksol: 0.382 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→500 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.4 % / Rfactor obs: 0.212 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 37.2 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.304 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.26 |