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Yorodumi- PDB-1fwu: CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF MANNOSE RECEPTOR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fwu | |||||||||
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Title | CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF MANNOSE RECEPTOR COMPLEXED WITH 3-SO4-LEWIS(X) | |||||||||
Components | CYSTEINE-RICH DOMAIN OF MANNOSE RECEPTOR | |||||||||
Keywords | SUGAR BINDING PROTEIN / beta trefoil / mannose receptor / sulfated carbohydrate | |||||||||
Function / homology | Function and homology information Cross-presentation of soluble exogenous antigens (endosomes) / cargo receptor activity / D-mannose binding / cellular response to interleukin-4 / receptor-mediated endocytosis / cellular response to type II interferon / transmembrane signaling receptor activity / signaling receptor activity / cellular response to lipopolysaccharide / endosome membrane ...Cross-presentation of soluble exogenous antigens (endosomes) / cargo receptor activity / D-mannose binding / cellular response to interleukin-4 / receptor-mediated endocytosis / cellular response to type II interferon / transmembrane signaling receptor activity / signaling receptor activity / cellular response to lipopolysaccharide / endosome membrane / cell surface / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Liu, Y. / Misulovin, Z. / Bjorkman, P.J. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: The molecular mechanism of sulfated carbohydrate recognition by the cysteine-rich domain of mannose receptor. Authors: Liu, Y. / Misulovin, Z. / Bjorkman, P.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fwu.cif.gz | 40.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fwu.ent.gz | 30.2 KB | Display | PDB format |
PDBx/mmJSON format | 1fwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fwu_validation.pdf.gz | 447.7 KB | Display | wwPDB validaton report |
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Full document | 1fwu_full_validation.pdf.gz | 451 KB | Display | |
Data in XML | 1fwu_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | 1fwu_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/1fwu ftp://data.pdbj.org/pub/pdb/validation_reports/fw/1fwu | 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: 15445.328 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN OF MANNOSE RECEPTOR Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH 3-SO4-LEWIS(X) / Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): 293 CELLS / Production host: Sus scrofa (pig) / References: PIR: A48925, UniProt: Q61830*PLUS |
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#2: Polysaccharide | alpha-L-fucopyranose-(1-3)-[3-O-sulfo-beta-D-galactopyranose-(1-4)]methyl 2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[3-O-sulfo-beta-D-galactopyranose-(1-4)]methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside Source method: isolated from a genetically manipulated source |
#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: 2.66 Å3/Da / Density % sol: 53.7 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8000, (NH4)2SO4, ph 6.5 - 7.5, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Dec 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 13916 / Num. obs: 13262 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.123 / % possible all: 86.8 |
Reflection | *PLUS Num. measured all: 108934 |
Reflection shell | *PLUS % possible obs: 86.6 % / Mean I/σ(I) obs: 9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 6.4 % / Rfactor obs: 0.213 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |