+Open data
-Basic information
Entry | Database: PDB / ID: 1tlg | ||||||
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Title | STRUCTURE OF A TUNICATE C-TYPE LECTIN COMPLEXED WITH D-GALACTOSE | ||||||
Components | POLYANDROCARPA LECTIN | ||||||
Keywords | LECTIN / C-TYPE LECTIN / GALACTOSE-SPECIFIC / CARBOHYDRATE BINDING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Polyandrocarpa misakiensis (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Poget, S.F. / Legge, G.B. / Bycroft, M. / Williams, R.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: The structure of a tunicate C-type lectin from Polyandrocarpa misakiensis complexed with D -galactose. Authors: Poget, S.F. / Legge, G.B. / Proctor, M.R. / Butler, P.J. / Bycroft, M. / Williams, R.L. #1: Journal: Roux'S Arch.Dev.Biol. / Year: 1995 Title: Expression of Genes for 2 C-Type Lectins During Budding of the Ascidian Polyandrocarpa-Misakiensis Authors: Shimada, M. / Fujiwara, S. / Kawamura, K. #2: Journal: DEVELOPMENT / Year: 1991 Title: Budding-Specific Lectin Induced in Epithelial Cells is an Extracellular Matrix Component for Stem Cell Aggregation in Tunicates Authors: Kawamura, K. / Fujiwara, S. / Sugino, Y.M. #3: Journal: J.Biol.Chem. / Year: 1990 Title: A Calcium-Dependent Galactose-Binding Lectin from the Tunicate Polyandrocarpa Misakiensis. Isolation, Characterization, and Amino Acid Sequence Authors: Suzuki, T. / Takagi, T. / Furukohri, T. / Kawamura, K. / Nakauchi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tlg.cif.gz | 63.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tlg.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 1tlg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tlg_validation.pdf.gz | 386.7 KB | Display | wwPDB validaton report |
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Full document | 1tlg_full_validation.pdf.gz | 387.7 KB | Display | |
Data in XML | 1tlg_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 1tlg_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/1tlg ftp://data.pdbj.org/pub/pdb/validation_reports/tl/1tlg | HTTPS FTP |
-Related structure data
Related structure data | 1byfSC 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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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.1639, -0.0514, -0.9851), Vector: |
-Components
#1: Protein | Mass: 14042.505 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Polyandrocarpa misakiensis (invertebrata) Description: SYNTHETIC GENE / Plasmid: PRSETA-LEC Cellular location (production host): CYTOPLASM AS INCLUSION BODIES Gene (production host): TC14-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): C41 / References: UniProt: P16108 #2: Sugar | #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
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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: 2.8 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1998 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→16.4 Å / Num. obs: 16111 / % possible obs: 99.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 23.14 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.171 / % possible all: 83.8 |
Reflection | *PLUS Num. measured all: 108587 |
Reflection shell | *PLUS % possible obs: 83.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BYF Resolution: 2.2→26 Å / SU B: 6.24 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.23 Details: ELECTRON DENSITY FOR RESIDUE MET A 1 AND MET B 1 IS PRESENT, BUT MODELLING WITH ACCEPTABLE GEOMETRY WAS NOT POSSIBLE. A CHAIN OF 5 VERY HIGH ELECTRON DENSITY SPHERES ADJACENT AND ORTHOGONAL ...Details: ELECTRON DENSITY FOR RESIDUE MET A 1 AND MET B 1 IS PRESENT, BUT MODELLING WITH ACCEPTABLE GEOMETRY WAS NOT POSSIBLE. A CHAIN OF 5 VERY HIGH ELECTRON DENSITY SPHERES ADJACENT AND ORTHOGONAL TO THE SIDE-CHAIN OF ASP A 2 AND ASP B 2 WAS MODELLED AS ZN-HOH-ZN-HOH-ZN, BUT THE RESOLUTION IS NOT HIGH ENOUGH FOR UNAMBIGUOUS CHARACTERISATION.
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Displacement parameters | Biso mean: 25.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→26 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.211 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |