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Yorodumi- PDB-2fdm: Crystal structure of the ternary complex of signalling glycoprote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fdm | |||||||||
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Title | Crystal structure of the ternary complex of signalling glycoprotein frm sheep (SPS-40)with hexasaccharide (NAG6) and peptide Trp-Pro-Trp at 3.0A resolution | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / TERNARY COMPLEX / SPS-40 / NAG6 / WPW / TRIPEPTIDE | |||||||||
Function / homology | Function and homology information response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / lung development / positive regulation of angiogenesis ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / lung development / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate binding / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / carbohydrate metabolic process / inflammatory response / apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / cytoplasm Similarity search - Function | |||||||||
Biological species | Ovis aries (sheep) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Srivastava, D.B. / Ethayathulla, A.S. / Kumar, J. / Somvanshi, R.K. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: To be Published Title: Crystal structure of the ternary complex of signalling glycoprotein frm sheep (SPS-40) with hexasaccharide (NAG6) and peptide Trp-Pro-Trp at 3.0A resolution Authors: Srivastava, D.B. / Ethayathulla, A.S. / Kumar, J. / Somvanshi, R.K. / Sharma, S. / Dey, S. / Singh, T.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fdm.cif.gz | 90.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fdm.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 2fdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/2fdm ftp://data.pdbj.org/pub/pdb/validation_reports/fd/2fdm | HTTPS FTP |
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-Related structure data
Related structure data | 1r2v S: Starting model for refinement |
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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: 40612.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Strain: Milk ,Mammary gland / References: UniProt: Q6TMG6 |
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#2: Protein/peptide | Mass: 487.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized |
#3: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: 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: 2.72 Å3/Da / Density % sol: 54.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 25mM tris-HCl, 11% ethanol , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 22, 2005 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 9481 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 58.8 Å2 / Rsym value: 0.11 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 3→3.12 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.282 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1r2v 1r2v Resolution: 3→19.88 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1099173.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.172 Å2 / ksol: 0.414954 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 6
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Xplor file |
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