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Yorodumi- PDB-5obt: Fully activated A. thaliana legumain isoform gamma in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5obt | |||||||||
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Title | Fully activated A. thaliana legumain isoform gamma in complex with Ac-YVAD-CMK | |||||||||
Components |
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Keywords | HYDROLASE / Legumain / Asparaginyl endopeptidase / Vacuolar processing enzyme / peptide cyclase | |||||||||
Function / homology | Function and homology information lytic vacuole / protein storage vacuole / legumain / response to ethylene / response to salicylic acid / leaf senescence / vacuolar protein processing / response to jasmonic acid / proteolysis involved in protein catabolic process / response to wounding ...lytic vacuole / protein storage vacuole / legumain / response to ethylene / response to salicylic acid / leaf senescence / vacuolar protein processing / response to jasmonic acid / proteolysis involved in protein catabolic process / response to wounding / endopeptidase activity / cysteine-type endopeptidase activity Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Zauner, B.F. / Dall, E. / Brandstetter, H. | |||||||||
Funding support | Austria, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structural analyses ofArabidopsis thalianalegumain gamma reveal differential recognition and processing of proteolysis and ligation substrates. Authors: Zauner, F.B. / Elsasser, B. / Dall, E. / Cabrele, C. / Brandstetter, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5obt.cif.gz | 143.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5obt.ent.gz | 108.9 KB | Display | PDB format |
PDBx/mmJSON format | 5obt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5obt_validation.pdf.gz | 458.3 KB | Display | wwPDB validaton report |
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Full document | 5obt_full_validation.pdf.gz | 460.3 KB | Display | |
Data in XML | 5obt_validation.xml.gz | 29.4 KB | Display | |
Data in CIF | 5obt_validation.cif.gz | 44.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/5obt ftp://data.pdbj.org/pub/pdb/validation_reports/ob/5obt | HTTPS FTP |
-Related structure data
Related structure data | 5nijS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26987.801 Da / Num. of mol.: 2 / Fragment: Cleaved N-terminus, UNP residues 56-283 Source method: isolated from a genetically manipulated source Details: Residue D176 is found to be converted to SNN / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g32940, F26P21.60 / Production host: Leishmania tarentolae (eukaryote) / References: UniProt: Q39119, legumain #2: Protein | Mass: 5766.393 Da / Num. of mol.: 2 / Fragment: Cleaved C-terminus, UNP Residues 284-334 Source method: isolated from a genetically manipulated source Details: Residue D176 is found to be converted to SNN / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g32940, F26P21.60 / Production host: Leishmania tarentolae (eukaryote) / References: UniProt: Q39119, legumain #3: Protein/peptide | #4: Water | ChemComp-HOH / | Has protein modification | 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: 1.9 Å3/Da / Density % sol: 35.33 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 4% PEG 4000, 100 mM sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→24.56 Å / Num. obs: 74201 / % possible obs: 93.5 % / Redundancy: 2.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.05 / Rrim(I) all: 0.07 / Net I/σ(I): 8.3 |
Reflection shell | Highest resolution: 1.5 Å / Redundancy: 2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.7 / Num. unique all: 7215 / Num. unique obs: 3597 / CC1/2: 0.78 / Rpim(I) all: 0.24 / Rrim(I) all: 0.34 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5nij Resolution: 1.5→24.558 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→24.558 Å
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Refine LS restraints |
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LS refinement shell |
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