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Yorodumi- PDB-5z37: Crystal Structure of Abrin A chain (Recombinant) at 1.3 Angstroms -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z37 | ||||||
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Title | Crystal Structure of Abrin A chain (Recombinant) at 1.3 Angstroms | ||||||
Components | Abrin A-chain | ||||||
Keywords | HYDROLASE / Ribosome Inactivating Protein | ||||||
Function / homology | Function and homology information galactose binding / rRNA N-glycosylase / rRNA N-glycosylase activity / positive regulation of endocytosis / defense response / toxin activity / carbohydrate binding / negative regulation of translation Similarity search - Function | ||||||
Biological species | Abrus precatorius (Indian licorice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Bansia, H. / Karande, A.A. / Ramakumar, S. | ||||||
Citation | Journal: FEBS J. / Year: 2019 Title: Structural basis for neutralization of cytotoxic abrin by monoclonal antibody D6F10. Authors: Bansia, H. / Bagaria, S. / Karande, A.A. / Ramakumar, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z37.cif.gz | 118.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z37.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 5z37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/5z37 ftp://data.pdbj.org/pub/pdb/validation_reports/z3/5z37 | HTTPS FTP |
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-Related structure data
Related structure data | 5z3iC 5z3jC 1abrS 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: 29707.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Abrus precatorius (Indian licorice) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7DM12, UniProt: P11140*PLUS |
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#2: Chemical | ChemComp-IMD / |
#3: Water | ChemComp-HOH / |
Sequence details | Authors state that the conflict (Y85H) is due to an ISOFORM OF Q7DM12 (ABRIN-A), but the isoform ...Authors state that the conflict (Y85H) is due to an ISOFORM OF Q7DM12 (ABRIN-A), but the isoform has not been reported in UniProt DB. FOR REFERENCE : Hung, C. H., Lee, M. C., Lee, T. C. & Lin, J. Y. (1993) Primary structure of three distinct isoabrins determined by cDNA sequencing : conservation and significance, J. Mol. Biol. 229,263 - 267 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 42.18 % |
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Crystal grow | Temperature: 295.15 K / Method: microbatch / pH: 6.5 / Details: 0.2M Magnesium Chloride, 20% PEG 8K, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å | ||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2014 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.3→27.63 Å / Num. obs: 57887 / % possible obs: 91.7 % / Redundancy: 7 % / Biso Wilson estimate: 13.96 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.05 / Net I/σ(I): 18.3 / Num. measured all: 405186 / Scaling rejects: 365 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ABR Resolution: 1.3→27.198 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.09 Å2 / Biso mean: 21.3698 Å2 / Biso min: 9.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→27.198 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21
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