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Yorodumi- PDB-5zwp: Crystal structure of the delta-class glutathione transferase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zwp | ||||||
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Title | Crystal structure of the delta-class glutathione transferase from Musca domestica | ||||||
Components | Glutathione S-transferase 1 | ||||||
Keywords | TRANSFERASE / isozyme / detoxification / housefly / GST | ||||||
Function / homology | Function and homology information glutathione transferase / glutathione transferase activity / glutathione metabolic process Similarity search - Function | ||||||
Biological species | Musca domestica (house fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Sue, M. / Yajima, S. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2018 Title: Crystal structure of the delta-class glutathione transferase in Musca domestica Authors: Sue, M. / Yajima, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zwp.cif.gz | 182 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zwp.ent.gz | 143.6 KB | Display | PDB format |
PDBx/mmJSON format | 5zwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zwp_validation.pdf.gz | 944.2 KB | Display | wwPDB validaton report |
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Full document | 5zwp_full_validation.pdf.gz | 946.6 KB | Display | |
Data in XML | 5zwp_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 5zwp_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/5zwp ftp://data.pdbj.org/pub/pdb/validation_reports/zw/5zwp | HTTPS FTP |
-Related structure data
Related structure data | 1jlvS 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: 23644.275 Da / Num. of mol.: 2 / Mutation: F173I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Musca domestica (house fly) / Gene: Gst1, Gst-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28338, glutathione transferase #2: Chemical | #3: Chemical | ChemComp-FMT / #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: 2.42 Å3/Da / Density % sol: 49.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2 M sodium citrate, pH 5.6, 1.8 M ammonium sulfate, 0.1 M tartrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 14, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→49.03 Å / Num. obs: 84246 / % possible obs: 95.9 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 11834 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JLV Resolution: 1.4→49.03 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.585 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.056 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.854 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→49.03 Å
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Refine LS restraints |
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