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Yorodumi- PDB-5o3v: Structural characterization of the fast and promiscuous macrocycl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o3v | |||||||||
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Title | Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to Presegetalin B1 | |||||||||
Components |
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Keywords | HYDROLASE / segetalin biosynthesis / prolyl oligopeptidase / macrocyclase / peptidase / beta-propeller / closed form | |||||||||
Function / homology | Function and homology information oligopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Vaccaria hispanica (bladder-soapwort) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | |||||||||
Authors | Ludewig, H. / Czekster, C.M. / Bent, A.F. / Naismith, J.H. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Characterization of the Fast and Promiscuous Macrocyclase from Plant PCY1 Enables the Use of Simple Substrates. Authors: Ludewig, H. / Czekster, C.M. / Oueis, E. / Munday, E.S. / Arshad, M. / Synowsky, S.A. / Bent, A.F. / Naismith, J.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o3v.cif.gz | 595.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o3v.ent.gz | 494.8 KB | Display | PDB format |
PDBx/mmJSON format | 5o3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o3v_validation.pdf.gz | 460.4 KB | Display | wwPDB validaton report |
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Full document | 5o3v_full_validation.pdf.gz | 466.8 KB | Display | |
Data in XML | 5o3v_validation.xml.gz | 49.9 KB | Display | |
Data in CIF | 5o3v_validation.cif.gz | 69.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/5o3v ftp://data.pdbj.org/pub/pdb/validation_reports/o3/5o3v | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 82483.266 Da / Num. of mol.: 2 / Mutation: S562A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccaria hispanica (bladder-soapwort) / Gene: Pcy1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4P353 #2: Protein/peptide | Mass: 3279.739 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccaria hispanica (bladder-soapwort) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F6LNL6 #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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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: 2.35 Å3/Da / Density % sol: 47.76 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: PCY1-S562A complex with PresegB1 was crystallized at 13.3 mg/mL with 0.163 mM PresegB1 in 34.5% (w/v) PEG 3350 and 70 mM Mg sulfate. For cryo protection 5 % (v/v) glycerol were added to reservoir solution. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→47.62 Å / Num. obs: 80090 / % possible obs: 99.5 % / Redundancy: 3.4 % / Net I/σ(I): 10.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→47.62 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU B: 16.156 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.213 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.405 Å2
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Refinement step | Cycle: 1 / Resolution: 2.17→47.62 Å
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Refine LS restraints |
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