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Yorodumi- PDB-7f5p: The crystal structure of VyPAL2-C214A, a dead mutant of VyPAL2 pe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f5p | |||||||||
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Title | The crystal structure of VyPAL2-C214A, a dead mutant of VyPAL2 peptide asparaginyl ligase in form I | |||||||||
Components | Peptide Asparaginyl Ligases | |||||||||
Keywords | PLANT PROTEIN / AEP / PAL / Legumain / Peptide ligase | |||||||||
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: 1.9 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 | 7f5p.cif.gz | 142.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f5p.ent.gz | 111.6 KB | Display | PDB format |
PDBx/mmJSON format | 7f5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f5p_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7f5p_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 7f5p_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 7f5p_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/7f5p ftp://data.pdbj.org/pub/pdb/validation_reports/f5/7f5p | HTTPS FTP |
-Related structure data
Related structure data | 7f5jC 7f5qC 7fa0C 6idvS C: citing same article (ref.) S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 31862.428 Da / Num. of mol.: 1 / Mutation: C214A 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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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #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: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #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: 2.64 Å3/Da / Density % sol: 53.42 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M lithium sulfate, 0.1 M sodium acetate, pH 4.6, 30% PEG 8000 |
-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: 0.95373 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40.91 Å / Num. obs: 26508 / % possible obs: 99.3 % / Redundancy: 26.5 % / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 8.85 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 19.2 % / Mean I/σ(I) obs: 0.68 / Num. unique obs: 2523 / CC1/2: 0.543 / % possible all: 97.63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IDV Resolution: 1.9→40.91 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.154 / Cross valid method: FREE R-VALUE / SU R Blow DPI: 0.152 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.132
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Displacement parameters | Biso mean: 72.89 Å2
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Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→40.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.91 Å
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Refinement TLS params. | Origin x: 13.6714 Å / Origin y: 0.7787 Å / Origin z: 17.694 Å
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Refinement TLS group | Selection details: { A|* } |