+Open data
-Basic information
Entry | Database: PDB / ID: 1g8w | ||||||
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Title | IMPROVED STRUCTURE OF PHYTOHEMAGGLUTININ-L FROM THE KIDNEY BEAN | ||||||
Components | LEUCOAGGLUTINATING PHYTOHEMAGGLUTININ | ||||||
Keywords | SUGAR BINDING PROTEIN / JELLY-ROLL FOLD / LEGUME LECTIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Phaseolus vulgaris (French bean) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Buts, L. / Hamelryck, T.W. / Dao-Thi, M. / Loris, R. / Wyns, L. / Etzler, M.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Weak protein-protein interactions in lectins: the crystal structure of a vegetative lectin from the legume Dolichos biflorus. Authors: Buts, L. / Dao-Thi, M.H. / Loris, R. / Wyns, L. / Etzler, M. / Hamelryck, T. #1: Journal: J.Biol.Chem. / Year: 1996 Title: The crystallographic structure of phytohemagglutinin-L Authors: Hamelryck, T.W. / Dao-Thi, M. / Poortmans, F. / Chrispeels, M.J. / Wyns, L. / Loris, R. #2: Journal: Proteins / Year: 1996 Title: Crystallisation of glycosylated and non-glycosylated phytohemagglutinin-L Authors: Dao-Thi, M. / Hamelryck, T.W. / Poortmans, F. / Voelker, T.A. / Chrispeels, M.J. / Wyns, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g8w.cif.gz | 188.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g8w.ent.gz | 150.2 KB | Display | PDB format |
PDBx/mmJSON format | 1g8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g8w_validation.pdf.gz | 477.6 KB | Display | wwPDB validaton report |
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Full document | 1g8w_full_validation.pdf.gz | 498.8 KB | Display | |
Data in XML | 1g8w_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 1g8w_validation.cif.gz | 46.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/1g8w ftp://data.pdbj.org/pub/pdb/validation_reports/g8/1g8w | HTTPS FTP |
-Related structure data
Related structure data | 1g7yC 1g9fC 1lesS 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: 25397.959 Da / Num. of mol.: 4 / Fragment: LEUCOAGGLUTINATING FRACTION OF THE SEED LECTIN / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (French bean) / Organ: SEED / References: UniProt: P05087 #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-CA / #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: 2.85 Å3/Da / Density % sol: 56.89 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 5 mg/ml protein; 100 mM TRIS/HCl; 8% (w/v) PEG(6000), pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Aug 1, 1995 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→10 Å / Num. all: 105939 / Num. obs: 100006 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 3.8 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 11.23 |
Reflection shell | Resolution: 2.8→2.95 Å / Mean I/σ(I) obs: 3.2 / % possible all: 82.1 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. all: 100006 / Num. obs: 26546 / Num. measured all: 105939 |
Reflection shell | *PLUS % possible obs: 82.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LES (lentil lectin) Resolution: 2.8→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3547881.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 19.88 Å2 / ksol: 0.262 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 9.9 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.3 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.31 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.28 |