+Open data
-Basic information
Entry | Database: PDB / ID: 6xt5 | |||||||||
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Title | Jack bean asparaginyl endopeptidase | |||||||||
Components | Legumain | |||||||||
Keywords | PLANT PROTEIN / Hydrolase / Asparaginyl endopeptidase | |||||||||
Function / homology | Legumain beta / legumain / Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family / proteolysis involved in protein catabolic process / cysteine-type endopeptidase activity / Legumain Function and homology information | |||||||||
Biological species | Canavalia ensiformis (jack bean) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å | |||||||||
Authors | Nonis, S.G. / Haywood, J. / Schmidberger, J.W. / Bond, C.S. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Plant Cell / Year: 2021 Title: Structural and biochemical analyses of concanavalin A circular permutation by jack bean asparaginyl endopeptidase. Authors: Nonis, S.G. / Haywood, J. / Schmidberger, J.W. / Mackie, E.R.R. / Soares da Costa, T.P. / Bond, C.S. / Mylne, J.S. #1: Journal: Biorxiv / Year: 2020 Title: Structural basis for a natural circular permutation in proteins Authors: Nonis, S.G. / Haywood, J. / Schmidberger, J.W. / Bond, C.S. / Mylne, J.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xt5.cif.gz | 185.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xt5.ent.gz | 141.6 KB | Display | PDB format |
PDBx/mmJSON format | 6xt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xt5_validation.pdf.gz | 444.1 KB | Display | wwPDB validaton report |
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Full document | 6xt5_full_validation.pdf.gz | 457.3 KB | Display | |
Data in XML | 6xt5_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 6xt5_validation.cif.gz | 42.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/6xt5 ftp://data.pdbj.org/pub/pdb/validation_reports/xt/6xt5 | HTTPS FTP |
-Related structure data
Related structure data | 6xt6C 5nijS 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: 50064.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canavalia ensiformis (jack bean) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle Express / References: UniProt: P49046, legumain #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: HEPES, PEG 20,000, EDTA disodium salt dihydrate / PH range: 7.5 - 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.984 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→46.33 Å / Num. obs: 26353 / % possible obs: 98.8 % / Redundancy: 3.4 % / CC1/2: 0.997 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.69→2.82 Å / Num. unique obs: 3311 / CC1/2: 0.662 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NIJ Resolution: 2.69→45.611 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.183 / SU B: 19.622 / SU ML: 0.37 / Average fsc free: 0.8219 / Average fsc work: 0.8491 / Cross valid method: FREE R-VALUE / ESU R Free: 0.384 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.426 Å2
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Refinement step | Cycle: LAST / Resolution: 2.69→45.611 Å
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Refine LS restraints |
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LS refinement shell |
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