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Yorodumi- PDB-1nko: Energetic and structural basis of sialylated oligosaccharide reco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nko | ||||||
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Title | Energetic and structural basis of sialylated oligosaccharide recognition by the natural killer cell inhibitory receptor p75/AIRM1 or Siglec-7 | ||||||
Components | Sialic acid binding Ig-like lectin 7 | ||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin / Siglec7 | ||||||
Function / homology | Function and homology information sialic acid binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / carbohydrate binding / cell adhesion / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Dimasi, N. / Attril, H. / van Aalten, D.M.F. / Moretta, L. / Biassoni, R. / Mariuzza, R.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure of the saccharide-binding domain of the human natural killer cell inhibitory receptor p75/AIRM1. Authors: Dimasi, N. / Moretta, A. / Moretta, L. / Biassoni, R. / Mariuzza, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nko.cif.gz | 37.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nko.ent.gz | 24.9 KB | Display | PDB format |
PDBx/mmJSON format | 1nko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nko_validation.pdf.gz | 431.4 KB | Display | wwPDB validaton report |
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Full document | 1nko_full_validation.pdf.gz | 435 KB | Display | |
Data in XML | 1nko_validation.xml.gz | 7 KB | Display | |
Data in CIF | 1nko_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/1nko ftp://data.pdbj.org/pub/pdb/validation_reports/nk/1nko | HTTPS FTP |
-Related structure data
Related structure data | 1qfoS 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: 15262.995 Da / Num. of mol.: 1 / Fragment: N-terminal IgV-like domain residues 19-150 / Mutation: Q55D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIGLEC7 OR AIRM1 / Plasmid: p75-1D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9Y286 |
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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: 1.94 Å3/Da / Density % sol: 36.43 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 4.2 Details: PEG 4000 20%, NaCl 0.2 M, 0.1 M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 5.5 / Method: vapor diffusion, hanging drop / Details: Dimasi, N., (2003) Acta Crystallogr., D59, 1856. | ||||||||||||||||||||||||||||||||||||||||||
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: CHESS / Beamline: F1 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→15 Å / Num. obs: 19800 / % possible obs: 75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 19.8 Å2 |
Reflection shell | Resolution: 1.45→15 Å / % possible all: 95.3 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. obs: 20819 / % possible obs: 89.3 % / Num. measured all: 238401 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Lowest resolution: 1.51 Å / % possible obs: 68.6 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QFO Resolution: 1.45→14.93 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.3265 Å2 / ksol: 0.44952 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.5 Å2
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Refine analyze | Luzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.21 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→14.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.54 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 4 % / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.171 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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