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Yorodumi- PDB-7f5q: The crystal structure of VyPAL2 peptide asparaginyl ligase in its... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f5q | |||||||||
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Title | The crystal structure of VyPAL2 peptide asparaginyl ligase in its active enzyme form | |||||||||
Components | Peptide Asparaginyl Ligases | |||||||||
Keywords | PLANT PROTEIN / AEP / Legumain / VyPAL2 | |||||||||
Function / homology | Function and homology information vacuolar protein processing / vacuole / 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: 2.3 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 | 7f5q.cif.gz | 139.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f5q.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 7f5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/7f5q ftp://data.pdbj.org/pub/pdb/validation_reports/f5/7f5q | HTTPS FTP |
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-Related structure data
Related structure data | 7f5jC 7f5pC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 51 - 329 / Label seq-ID: 2 - 279
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31132.846 Da / Num. of mol.: 2 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 | 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: Sugar | |
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-Non-polymers , 2 types, 370 molecules
#5: Chemical | ChemComp-EDO / #6: 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: 2.47 Å3/Da / Density % sol: 50.18 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 0.2 M lithium sulfate, 0.1 M sodium acetate, pH 4.5, 30% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.99999 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.88 Å / Num. obs: 28255 / % possible obs: 99.96 % / Redundancy: 10.3 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.419 / Net I/σ(I): 7.51 |
Reflection shell | Resolution: 2.3→2.382 Å / Redundancy: 10.4 % / Rmerge(I) obs: 2.141 / Mean I/σ(I) obs: 1.32 / Num. unique obs: 2779 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IDV Resolution: 2.3→48.88 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.862 / SU ML: 0.179 / Cross valid method: FREE R-VALUE / ESU R: 0.331 / ESU R Free: 0.215 / Details: Hydrogens have not been used
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.69 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→48.88 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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