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Yorodumi- PDB-6tho: Acylintermediate of glutathione and the mature primitive phytoche... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tho | ||||||
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Title | Acylintermediate of glutathione and the mature primitive phytochelatin synthase Alr0975 from Nostoc PCC 7120 at atomic resolution. | ||||||
Components | Alr0975 protein | ||||||
Keywords | TRANSFERASE / glutathione / phytochelatin / detoxification / chelating heavy atoms | ||||||
Function / homology | Function and homology information glutathione gamma-glutamylcysteinyltransferase / glutathione gamma-glutamylcysteinyltransferase activity / phytochelatin biosynthetic process / response to metal ion / metal ion binding Similarity search - Function | ||||||
Biological species | Nostoc sp. PCC 7120 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å | ||||||
Authors | Feiler, C.G. / Blankenfeldt, W. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2022 Title: Structural and Biophysical Analysis of the Phytochelatin-Synthase-Like Enzyme from Nostoc sp. Shows That Its Protease Activity is Sensitive to the Redox State of the Substrate. Authors: Gisdon, F.J. / Feiler, C.G. / Kempf, O. / Foerster, J.M. / Haiss, J. / Blankenfeldt, W. / Ullmann, G.M. / Bombarda, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tho.cif.gz | 407.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tho.ent.gz | 282.2 KB | Display | PDB format |
PDBx/mmJSON format | 6tho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tho_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6tho_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6tho_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 6tho_validation.cif.gz | 44.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/6tho ftp://data.pdbj.org/pub/pdb/validation_reports/th/6tho | HTTPS FTP |
-Related structure data
Related structure data | 6th5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25067.400 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Gene: alr0975, alr0975 / Plasmid: p10$ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YY76 #2: Chemical | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 38.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 16.5% PEG 8000, 0.1M MES pH 5.5, 0.18 M CaAc, 5 mM glutathione cryoprotectant 20% glycerol PH range: 5-6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2013 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→29.21 Å / Num. obs: 164591 / % possible obs: 98.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 8.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05585 / Rpim(I) all: 0.03381 / Rrim(I) all: 0.06559 / Net I/σ(I): 12.06 |
Reflection shell | Resolution: 1.09→1.129 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4272 / Mean I/σ(I) obs: 2.72 / Num. unique obs: 55829 / CC1/2: 0.815 / Rpim(I) all: 0.2616 / Rrim(I) all: 0.5034 / % possible all: 99.33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TH5 Resolution: 1.09→29.21 Å / SU ML: 0.0786 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.4459 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.09→29.21 Å
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Refine LS restraints |
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LS refinement shell |
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