+Open data
-Basic information
Entry | Database: PDB / ID: 6lko | |||||||||
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Title | Turning an asparaginyl endopeptidase into a peptide ligase | |||||||||
Components | Asparaginyl endopeptidase | |||||||||
Keywords | HYDROLASE / AEP / Asparaginyl Endopeptidase / Peptide asparaginyl Ligase / PAL | |||||||||
Function / homology | Function and homology information legumain / vacuolar protein processing / proteolysis involved in protein catabolic process / cysteine-type endopeptidase activity Similarity search - Function | |||||||||
Biological species | Clitoria ternatea (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | El Sahili, A. / Lescar, J. | |||||||||
Funding support | Singapore, 1items
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Citation | Journal: Acs Catalysis / Year: 2020 Title: Turning an Asparaginyl Endopeptidase into a Peptide Ligase Authors: Hemu, X. / El Sahili, A. / Hu, S. / Zhang, X. / Serra, A. / Goh, B.C. / Darwis, D.A. / Chen, M.W. / Sze, S.K. / Liu, C.F. / Lescar, J. / Tam, J.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lko.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lko.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 6lko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lko_validation.pdf.gz | 472.8 KB | Display | wwPDB validaton report |
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Full document | 6lko_full_validation.pdf.gz | 476.7 KB | Display | |
Data in XML | 6lko_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 6lko_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/6lko ftp://data.pdbj.org/pub/pdb/validation_reports/lk/6lko | HTTPS FTP |
-Related structure data
Related structure data | 6l4vSC 6l4wC 6l4xC 6l4yC 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: 55789.918 Da / Num. of mol.: 1 / Mutation: P183A, G252V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clitoria ternatea (plant) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0P0QM28, legumain |
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#2: Sugar | ChemComp-NAG / |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% v/v PEG 500* MME, 10 % w/v PEG 20000, 0.1M Sodium formate, 0.1M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate, 0.1M Potassium sodium tartrate tetrahydrate, 0.1M Sodium ...Details: 20% v/v PEG 500* MME, 10 % w/v PEG 20000, 0.1M Sodium formate, 0.1M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate, 0.1M Potassium sodium tartrate tetrahydrate, 0.1M Sodium oxamate, 0.1M Sodium HEPES, MOPS (acid) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2→42.31 Å / Num. obs: 60392 / % possible obs: 99.96 % / Redundancy: 13 % / Biso Wilson estimate: 32.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.093 / Net I/σ(I): 22.66 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 1.076 / Num. unique obs: 3230 / CC1/2: 0.784 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6L4V Resolution: 2→42.31 Å / SU ML: 0.2248 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 21.3534 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→42.31 Å
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Refine LS restraints |
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LS refinement shell |
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