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Yorodumi- PDB-2zg3: Crystal Structure of Two N-terminal Domains of Native Siglec-5 in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zg3 | |||||||||
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Title | Crystal Structure of Two N-terminal Domains of Native Siglec-5 in Complex with 3'-Sialyllactose | |||||||||
Components | Sialic acid-binding Ig-like lectin 5 | |||||||||
Keywords | IMMUNE SYSTEM/CARBOHYDRATE BINDING PROTEIN / Siglec-5 inhibitory receptor / two-domain structure / V-set / C2-set / Ig-like domain / sialic acid / 3'-sialyllactose complex / Cell adhesion / Glycoprotein / Immunoglobulin domain / Lectin / Membrane / Polymorphism / Transmembrane / IMMUNE SYSTEM-CARBOHYDRATE BINDING PROTEIN COMPLEX | |||||||||
Function / homology | Function and homology information sialic acid binding / tertiary granule membrane / ficolin-1-rich granule membrane / secretory granule membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / carbohydrate binding / cell adhesion / Neutrophil degranulation / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Zhuravleva, M.A. / Sun, P.D. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural implications of Siglec-5-mediated sialoglycan recognition Authors: Zhuravleva, M.A. / Trandem, K. / Sun, P.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zg3.cif.gz | 59.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zg3.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zg3_validation.pdf.gz | 780.8 KB | Display | wwPDB validaton report |
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Full document | 2zg3_full_validation.pdf.gz | 794.5 KB | Display | |
Data in XML | 2zg3_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 2zg3_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/2zg3 ftp://data.pdbj.org/pub/pdb/validation_reports/zg/2zg3 | HTTPS FTP |
-Related structure data
Related structure data | 2zg1C 2zg2SC C: citing same article (ref.) 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: Antibody | Mass: 24332.354 Da / Num. of mol.: 1 Fragment: N-terminal V-set and C2-set domain, UNP residues 20-233 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIGLEC5 / Plasmid: pET30a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O15389 |
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#2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose 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: 3.66 Å3/Da / Density % sol: 66.42 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% MPEG 550, 0.1M TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 1, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 7405 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rsym value: 0.046 / Net I/σ(I): 34.3 |
Reflection shell | Highest resolution: 3 Å / Mean I/σ(I) obs: 4.6 / Rsym value: 0.36 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZG2 Resolution: 3→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 109 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.12 Å /
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Xplor file |
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