+Open data
-Basic information
Entry | Database: PDB / ID: 1avb | |||||||||
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Title | ARCELIN-1 FROM PHASEOLUS VULGARIS L | |||||||||
Components | ARCELIN-1 | |||||||||
Keywords | LECTIN / LECTIN-LIKE GLYCOPROTEIN / PLANT DEFENSE / INSECTICIDAL ACTIVITY | |||||||||
Function / homology | Function and homology information nutrient reservoir activity / defense response / toxin activity / carbohydrate binding Similarity search - Function | |||||||||
Biological species | Phaseolus vulgaris (French bean) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR, DENSITY MODIFICATION, MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Mourey, L. / Pedelacq, J.D. / Fabre, C. / Rouge, P. / Samama, J.P. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Crystal structure of the arcelin-1 dimer from Phaseolus vulgaris at 1.9-A resolution. Authors: Mourey, L. / Pedelacq, J.D. / Birck, C. / Fabre, C. / Rouge, P. / Samama, J.P. #1: Journal: Proteins / Year: 1997 Title: Small-Angle X-Ray Scattering and Crystallographic Studies of Arcelin-1: An Insecticidal Lectin-Like Glycoprotein from Phaseolus Vulgaris L Authors: Mourey, L. / Pedelacq, J.D. / Fabre, C. / Causse, H. / Rouge, P. / Samama, J.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1avb.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1avb.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 1avb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/1avb ftp://data.pdbj.org/pub/pdb/validation_reports/av/1avb | HTTPS FTP |
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-Related structure data
Related structure data | 1loeS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999998, -0.001916, 0.000892), Vector: |
-Components
#1: Protein | Mass: 24984.553 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (French bean) / Organ: SEED / Strain: CV. RAZ-2 / References: UniProt: P19329 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: Chemical | #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: 2.2 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.8 Details: PROTEIN WAS CRYSTALLIZED FROM 25% PEG400, 0.3 M AMMONIUM SULFATE IN 0.1 M MES BUFFER PH 4.8-4.9 PH range: 4.8-4.9 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging dropDetails: Mourey, L., (1997) Proteins: Struct.,Funct., Genet., 29, 433. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.938 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.938 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→33.7 Å / Num. obs: 41612 / % possible obs: 97.7 % / Redundancy: 3 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 7.5 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIR, DENSITY MODIFICATION, MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LOE Resolution: 1.9→33.71 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 Details: NCS CONSTRAINTS WERE APPLIED DURING REFINEMENT TO 2.5 ANGSTROMS RESOLUTION. THEY WERE LATER RELEASED AFTER RESOLUTION WAS EXTENDED TO 1.9 ANGSTROMS.
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Displacement parameters | Biso mean: 22.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→33.71 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: UNRESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.93 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 15
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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