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Yorodumi- PDB-7zva: Crystal Structure of the native zymogen form of the glutamic-clas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zva | ||||||
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Title | Crystal Structure of the native zymogen form of the glutamic-class prolyl-endopeptidase neprosin at 1.80 A resolution. | ||||||
Components | C-terminal peptidase | ||||||
Keywords | HYDROLASE / glutamic endopeptidase / zymogen / proform / coeliac disease therapy / plant protease | ||||||
Function / homology | ACETATE ION / ISOPROPYL ALCOHOL Function and homology information | ||||||
Biological species | Nepenthes ventricosa x Nepenthes alata (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Del Amo-Maestro, L. / Eckhard, U. / Rodriguez-Banqueri, A. / Mendes, S.R. / Guevara, T. / Gomis-Ruth, F.X. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Molecular and in vivo studies of a glutamate-class prolyl-endopeptidase for coeliac disease therapy. Authors: Del Amo-Maestro, L. / Mendes, S.R. / Rodriguez-Banqueri, A. / Garzon-Flores, L. / Girbal, M. / Rodriguez-Lagunas, M.J. / Guevara, T. / Franch, A. / Perez-Cano, F.J. / Eckhard, U. / Gomis-Ruth, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zva.cif.gz | 154 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zva.ent.gz | 119.4 KB | Display | PDB format |
PDBx/mmJSON format | 7zva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/7zva ftp://data.pdbj.org/pub/pdb/validation_reports/zv/7zva | HTTPS FTP |
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-Related structure data
Related structure data | 7zu8SC 7zvbC 7zvcC 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43006.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Pro-form of the glutamic endopeptidase neprosin (R25 to Q380) with an N-terminal IgK leader sequence and a C-terminal non-cleavable His6-tag. Source: (gene. exp.) Nepenthes ventricosa x Nepenthes alata (plant) Plasmid: pCMV-Sport 6 Cell line (production host): Suspension-adapted 293 human embryonic kidney (HEK) cells Production host: Homo sapiens (human) |
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-Sugars , 2 types, 2 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 |
-Non-polymers , 4 types, 270 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ACT / #6: Chemical | ChemComp-IPA / | #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: 1.99 Å3/Da / Density % sol: 38.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium acetate pH 4.0, 22% PEG 6000, 10% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 1.005 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.005 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→63.2 Å / Num. obs: 32321 / % possible obs: 99.3 % / Redundancy: 12.6 % / CC1/2: 0.999 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.8→1.864 Å / Num. unique obs: 2996 / CC1/2: 0.71 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ZU8 Resolution: 1.8→23.16 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.135 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.12
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Displacement parameters | Biso max: 82.44 Å2 / Biso mean: 35.76 Å2 / Biso min: 19.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→23.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 32
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Refinement TLS params. | Method: refined / Origin x: 28.1314 Å / Origin y: 12.7223 Å / Origin z: 43.3187 Å
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Refinement TLS group |
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