+Open data
-Basic information
Entry | Database: PDB / ID: 2zx4 | |||||||||
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Title | Rhamnose-binding lectin CSL3 | |||||||||
Components | CSL3 | |||||||||
Keywords | IMMUNE SYSTEM / SUGAR BINDING PROTEIN / LECTIN / RHAMNOSE / INNATE IMMUNITY | |||||||||
Function / homology | Function and homology information rhamnose binding / melibiose binding / cortical granule / galactose binding / NLS-dependent protein nuclear import complex / female germ cell nucleus / protein homodimerization activity / cytoplasm Similarity search - Function | |||||||||
Biological species | Oncorhynchus keta (chum salmon) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Shirai, T. / Watababe, Y. / Lee, M. / Ogawa, T. / Muramoto, K. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structure of rhamnose-binding lectin CSL3: unique pseudo-tetrameric architecture of a pattern recognition protein Authors: Shirai, T. / Watanabe, Y. / Lee, M.S. / Ogawa, T. / Muramoto, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zx4.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zx4.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 2zx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zx4_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2zx4_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2zx4_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 2zx4_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/2zx4 ftp://data.pdbj.org/pub/pdb/validation_reports/zx/2zx4 | HTTPS FTP |
-Related structure data
Related structure data | 2zx0SC 2zx1C 2zx2C 2zx3C 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: 21545.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oncorhynchus keta (chum salmon) / References: UniProt: P86179*PLUS #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE. | |
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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: 2.31 Å3/Da / Density % sol: 46.69 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: 15% PEG8000, 50mM potassium phosphate, pH4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Oct 27, 2008 / Details: mirrors |
Radiation | Monochromator: confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→8 Å / Num. all: 11113 / Num. obs: 10068 / % possible obs: 90.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.077 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.7→2.79 Å / Mean I/σ(I) obs: 7 / Num. unique all: 838 / Rsym value: 0.178 / % possible all: 77.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZX0 Resolution: 2.7→8 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.858 / SU B: 13.376 / SU ML: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.905 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.689→2.751 Å / Total num. of bins used: 20
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