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Yorodumi- PDB-1dqo: Crystal structure of the cysteine rich domain of mannose receptor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dqo | |||||||||
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Title | Crystal structure of the cysteine rich domain of mannose receptor complexed with Acetylgalactosamine-4-sulfate | |||||||||
Components | MANNOSE RECEPTOR | |||||||||
Keywords | SUGAR BINDING PROTEIN / beta trefoil / multilectin receptor / pituitary hormones / sulfated carbohydrate | |||||||||
Function / homology | Function and homology information Cross-presentation of soluble exogenous antigens (endosomes) / cargo receptor activity / mannose binding / receptor-mediated endocytosis / cellular response to interleukin-4 / 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 / mannose binding / receptor-mediated endocytosis / cellular response to interleukin-4 / 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: 2.2 Å | |||||||||
Authors | Liu, Y. / Chirino, A.J. / Misulovin, Z. / Leteux, C. / Feizi, T. / Nussenzweig, M.C. / Bjorkman, P.J. | |||||||||
Citation | Journal: J.Exp.Med. / Year: 2000 Title: Crystal structure of the cysteine-rich domain of mannose receptor complexed with a sulfated carbohydrate ligand. Authors: Liu, Y. / Chirino, A.J. / Misulovin, Z. / Leteux, C. / Feizi, T. / Nussenzweig, M.C. / 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 | 1dqo.cif.gz | 44.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dqo.ent.gz | 30.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/1dqo ftp://data.pdbj.org/pub/pdb/validation_reports/dq/1dqo | HTTPS FTP |
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-Related structure data
Related structure data | 1dqgSC 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: 15558.486 Da / Num. of mol.: 1 / Fragment: CYSTEINE RICH DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell: MACROPHAGE / Cell line: EPITHELIAL CELL / Production host: Homo sapiens (human) / References: UniProt: Q61830 |
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#2: Sugar | ChemComp-ASG / |
#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: 2.64 Å3/Da / Density % sol: 53.33 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000, ammonium sulfate, pH 6.5, 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: Oct 30, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. all: 8984 / Num. obs: 8984 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.105 / % possible all: 95.5 |
Reflection | *PLUS Num. measured all: 86630 |
Reflection shell | *PLUS % possible obs: 95.5 % / Mean I/σ(I) obs: 11.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DQG Resolution: 2.2→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→25 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 25 Å / σ(F): 0 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |