+Open data
-Basic information
Entry | Database: PDB / ID: 6l4w | |||||||||
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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: 1.66 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 | 6l4w.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l4w.ent.gz | 78.8 KB | Display | PDB format |
PDBx/mmJSON format | 6l4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l4w_validation.pdf.gz | 487.4 KB | Display | wwPDB validaton report |
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Full document | 6l4w_full_validation.pdf.gz | 490.1 KB | Display | |
Data in XML | 6l4w_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 6l4w_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/6l4w ftp://data.pdbj.org/pub/pdb/validation_reports/l4/6l4w | HTTPS FTP |
-Related structure data
Related structure data | 6l4vSC 6l4xC 6l4yC 6lkoC 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: 55815.953 Da / Num. of mol.: 1 / Mutation: G252V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clitoria ternatea (plant) Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) References: UniProt: A0A0P0QM28, legumain |
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#2: Sugar | ChemComp-NAG / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-PEG / |
#5: 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: 2.14 Å3/Da / Density % sol: 42.64 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7.2 Details: 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 HEPES, 0.1M MOPS, 10% Ethylen Glycol, 8% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91882 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91882 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→22.79 Å / Num. obs: 56975 / % possible obs: 98.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.07842 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.66→1.72 Å / Rmerge(I) obs: 1.722 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6L4V Resolution: 1.66→22.79 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.101 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.108 / SU Rfree Blow DPI: 0.104 / SU Rfree Cruickshank DPI: 0.099
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Displacement parameters | Biso mean: 32.65 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→22.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.72 Å
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