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Yorodumi- PDB-6nv6: Crystal structure of the theta class glutathione S-transferase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nv6 | ||||||
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Title | Crystal structure of the theta class glutathione S-transferase from the citrus canker pathogen Xanthomonas axonopodis pv. citri with glutathione bound | ||||||
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: 2.65 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 | 6nv6.cif.gz | 173.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nv6.ent.gz | 134.7 KB | Display | PDB format |
PDBx/mmJSON format | 6nv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nv6_validation.pdf.gz | 714.2 KB | Display | wwPDB validaton report |
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Full document | 6nv6_full_validation.pdf.gz | 724.3 KB | Display | |
Data in XML | 6nv6_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 6nv6_validation.cif.gz | 49.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/6nv6 ftp://data.pdbj.org/pub/pdb/validation_reports/nv/6nv6 | HTTPS FTP |
-Related structure data
Related structure data | 6nxvC 4kh7S 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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2 |
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4 |
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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: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q8PG02, glutathione transferase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-GSH / | #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: 3.25 Å3/Da / Density % sol: 62.17 % / Description: Needle-like crystal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.25 Details: 0.1M bis-tris:HCl, pH 7.0, 0.2M magnesium chloride and 25% (w/v) PEG 3,350 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: Sep 2, 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: 2.65→30 Å / Num. obs: 35328 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 25.263 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.063 / Rrim(I) all: 0.138 / Net I/av σ(I): 10.7 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2 / Num. unique obs: 5096 / CC1/2: 0.632 / Rpim(I) all: 0.496 / Rrim(I) all: 0.812 / % possible all: 99.1 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KH7 Resolution: 2.65→29.998 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.08 Å2 / Biso mean: 45.0081 Å2 / Biso min: 14.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.65→29.998 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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