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Open data
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Basic information
Entry | Database: PDB / ID: 1abr | |||||||||
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Title | CRYSTAL STRUCTURE OF ABRIN-A | |||||||||
![]() | (ABRIN-A) x 2 | |||||||||
![]() | GLYCOSIDASE/CARBOHYDRATE / GLYCOSIDASE-CARBOHYDRATE complex / LECTIN / LECTIN (AGGLUTININ) / GLYCOPROTEIN / PLANT SEED PROTEIN / PLANT TOXIN / PROTEIN SYNTHESIS INHIBITOR / TOXIN | |||||||||
Function / homology | ![]() galactose binding / rRNA N-glycosylase / rRNA N-glycosylase activity / positive regulation of endocytosis / defense response / toxin activity / negative regulation of translation Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Tahirov, T.H. / Lu, T.-H. / Liaw, Y.-C. / Chu, S.-C. / Lin, J.-Y. | |||||||||
![]() | ![]() Title: Crystal structure of abrin-a at 2.14 A. Authors: Tahirov, T.H. / Lu, T.H. / Liaw, Y.C. / Chen, Y.L. / Lin, J.Y. #1: ![]() Title: A New Crystal Form of Abrin-A from the Seeds of Abrus Precatorius Authors: Tahirov, T.H. / Lu, T.-H. / Liaw, Y.-C. / Chu, S.-C. / Lin, J.-Y. #2: ![]() Title: Primary Structure of Three Distinct Isobrins Determined by Cdna Sequencing: Conservation and Significance Authors: Hung, C.-H. / Lee, M.-C. / Lee, T.-C. / Lin, J.-Y. #3: ![]() Title: The Complete Amino Acid Sequence of the A-Chain of Abrin-1, a Toxic Protein from the Seeds of Abrus Precatorius Authors: Fanatsu, G. / Taguchi, Y. / Kamenosono, M. / Yanaka, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.5 KB | Display | ![]() |
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PDB format | ![]() | 118 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.8 KB | Display | |
Data in CIF | ![]() | 36 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 28124.326 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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#2: Protein | Mass: 30111.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source References: UniProt: P11140 |
#3: Polysaccharide | beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-L-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-glucopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.64 % | ||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 26964 / % possible obs: 78.7 % / Observed criterion σ(I): 1 |
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Processing
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Refinement | Resolution: 2.14→10 Å / σ(F): 2
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Displacement parameters | Biso mean: 30.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.189 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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