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Yorodumi- PDB-7f5j: The crystal structure of VyPAL2-I244V, a more efficient mutant of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f5j | |||||||||
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Title | The crystal structure of VyPAL2-I244V, a more efficient mutant of VyPAL2 peptide asparaginyl ligase in its active enzyme form | |||||||||
Components | Peptide Asparaginyl Ligases | |||||||||
Keywords | PLANT PROTEIN / AEP / Legumain / Peptide ligase / PAL | |||||||||
Function / homology | Function and homology information vacuolar protein processing / proteolysis involved in protein catabolic process / cysteine-type endopeptidase activity Similarity search - Function | |||||||||
Biological species | Viola philippica (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.593 Å | |||||||||
Authors | Hu, S. / Sahili, A. / Lescar, J. | |||||||||
Funding support | Singapore, 1items
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Citation | Journal: Plant Cell / Year: 2022 Title: Structural basis for proenzyme maturation, substrate recognition, and ligation by a hyperactive peptide asparaginyl ligase. Authors: Hu, S. / El Sahili, A. / Kishore, S. / Wong, Y.H. / Hemu, X. / Goh, B.C. / Zhipei, S. / Wang, Z. / Tam, J.P. / Liu, C.F. / Lescar, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f5j.cif.gz | 242.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f5j.ent.gz | 193.7 KB | Display | PDB format |
PDBx/mmJSON format | 7f5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f5j_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7f5j_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7f5j_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 7f5j_validation.cif.gz | 40.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/7f5j ftp://data.pdbj.org/pub/pdb/validation_reports/f5/7f5j | HTTPS FTP |
-Related structure data
Related structure data | 7f5pC 7f5qC 7fa0C 6idvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31118.818 Da / Num. of mol.: 2 / Mutation: I244V Source method: isolated from a genetically manipulated source Details: D171 (forming SNN), residue 172 is HD0 (HIS + SNN) / Source: (gene. exp.) Viola philippica (plant) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A509GV09 |
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-Sugars , 3 types, 6 molecules
#2: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 510 molecules
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.22 Å3/Da / Density % sol: 44.65 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5, 25% PEG 3350 |
-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: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.593→46.06 Å / Num. obs: 74533 / % possible obs: 99.26 % / Redundancy: 13.4 % / Biso Wilson estimate: 29.35 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08307 / Rpim(I) all: 0.02365 / Rrim(I) all: 0.08643 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.593→1.65 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 0.83 / Num. unique obs: 6869 / CC1/2: 0.449 / CC star: 0.787 / Rpim(I) all: 0.8825 / % possible all: 92.83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IDV Resolution: 1.593→46.06 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.081 / Cross valid method: FREE R-VALUE / SU R Blow DPI: 0.086 / SU Rfree Blow DPI: 0.085 / SU Rfree Cruickshank DPI: 0.082
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Displacement parameters | Biso mean: 37.91 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.593→46.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.593→1.61 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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