+Open data
-Basic information
Entry | Database: PDB / ID: 1uln | ||||||
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Title | Crystal Structure of Pokeweed Lectin-D1 | ||||||
Components | lectin-D | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin / chitin-binding domain | ||||||
Function / homology | Function and homology information chitin binding / positive regulation of cell division / positive regulation of mitotic nuclear division / carbohydrate binding Similarity search - Function | ||||||
Biological species | Phytolacca americana (American pokeweed) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Fujii, T. / Hayashida, M. / Hamasu, M. / Ishiguro, M. / Hata, Y. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structures of two lectins from the roots of pokeweed (Phytolacca americana). Authors: Fujii, T. / Hayashida, M. / Hamasu, M. / Ishiguro, M. / Hata, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uln.cif.gz | 29.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uln.ent.gz | 19.4 KB | Display | PDB format |
PDBx/mmJSON format | 1uln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uln_validation.pdf.gz | 410.2 KB | Display | wwPDB validaton report |
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Full document | 1uln_full_validation.pdf.gz | 411 KB | Display | |
Data in XML | 1uln_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 1uln_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/1uln ftp://data.pdbj.org/pub/pdb/validation_reports/ul/1uln | HTTPS FTP |
-Related 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: 9326.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phytolacca americana (American pokeweed) / Tissue: roots / References: UniProt: P83790 |
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#2: 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: 1.69 Å3/Da / Density % sol: 26.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, 0.2M calcium acetate, 0.1M sodium phosphate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 20, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40 Å / Num. all: 9068 / Num. obs: 9068 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.4 Å2 |
Reflection shell | Resolution: 1.65→1.75 Å / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→18.88 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 608320.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.04 Å2 / ksol: 0.378846 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→18.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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