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Yorodumi- PDB-6nxv: Crystal structure of the theta class glutathione S-transferase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nxv | ||||||
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Title | Crystal structure of the theta class glutathione S-transferase from the citrus canker pathogen Xanthomonas axonopodis pv. citri, apo form | ||||||
Components | Glutathione S-transferase | ||||||
Keywords | TRANSFERASE / theta class GST / glutathione S-transferase / citrus canker / plant pathogen / dehalogenase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Xanthomonas axonopodis pv. citri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å | ||||||
Authors | Hilario, E. / De Keyser, S. / Fan, L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Structural and biochemical characterization of a glutathione transferase from the citrus canker pathogen Xanthomonas. Authors: Hilario, E. / De Keyser, S. / Fan, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nxv.cif.gz | 163.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nxv.ent.gz | 126.3 KB | Display | PDB format |
PDBx/mmJSON format | 6nxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/6nxv ftp://data.pdbj.org/pub/pdb/validation_reports/nx/6nxv | HTTPS FTP |
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-Related structure data
Related structure data | 6nv6SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 22850.918 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria) Strain: 306 / Gene: gst, XAC3819 / Plasmid: pETSUMO / Details (production host): pETSUMO-XAC3819 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)pLys-S / References: UniProt: Q8PG02 #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-DMS / #4: 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: 3.13 Å3/Da / Density % sol: 60.66 % / Description: Needle-like crystal |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.1M Bis-Tris, pH 7.1, 0.2M magnesium chloride, 26% PEG 3,350. Crystals appear in 2-3 days and grow up to 6-7 days PH range: 7.0 - 7.25 / Temp details: constant |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Oxford Cobra CryoSystem / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 9, 2018 / Details: Varimax Confocal Max-Flux | |||||||||||||||||||||||||||
Radiation | Monochromator: Osmic Varimax HF ArcSec / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.75→80.439 Å / Num. all: 30033 / Num. obs: 30033 / % possible obs: 98.8 % / Redundancy: 5.3 % / Rpim(I) all: 0.063 / Rrim(I) all: 0.148 / Rsym value: 0.121 / Net I/av σ(I): 5.9 / Net I/σ(I): 8.9 / Num. measured all: 159325 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Phasing dm | Method: Solvent flattening and Histogram matching / Reflection: 29943 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NV6 Resolution: 2.75→29.813 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.1 Å2 / Biso mean: 47.9007 Å2 / Biso min: 23.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→29.813 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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