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Yorodumi- PDB-6j3e: Crystal structure of an apo form of the glutathione S-transferase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j3e | |||||||||||||||
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Title | Crystal structure of an apo form of the glutathione S-transferase, CsGST63524, of Ceriporiopsis subvermispora | |||||||||||||||
Components | glutathione S-transferase | |||||||||||||||
Keywords | TRANSFERASE / glutathione S-transferase / Ceriporiopsis subvermispora | |||||||||||||||
Function / homology | Function and homology information Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin ...Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | |||||||||||||||
Biological species | Ceriporiopsis subvermispora (fungus) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.455 Å | |||||||||||||||
Authors | Osman, W.H.W. / Mikami, B. / Saka, N. / Kondo, K. / Nagata, T. / Katahira, M. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2019 Title: Structure of a serine-type glutathione S-transferase of Ceriporiopsis subvermispora and identification of the enzymatically important non-canonical residues by functional mutagenesis. Authors: Osman, W.H.W. / Mikami, B. / Saka, N. / Kondo, K. / Nagata, T. / Katahira, M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j3e.cif.gz | 114 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j3e.ent.gz | 87.5 KB | Display | PDB format |
PDBx/mmJSON format | 6j3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j3e_validation.pdf.gz | 453.5 KB | Display | wwPDB validaton report |
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Full document | 6j3e_full_validation.pdf.gz | 459.6 KB | Display | |
Data in XML | 6j3e_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 6j3e_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/6j3e ftp://data.pdbj.org/pub/pdb/validation_reports/j3/6j3e | HTTPS FTP |
-Related structure data
Related structure data | 6j3fC 4f03S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28763.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ceriporiopsis subvermispora (strain B) (fungus) Gene: CsMn06, CERSUDRAFT_63524 / Production host: Escherichia coli (E. coli) / References: UniProt: M2R618 #2: Chemical | ChemComp-EDO / #3: 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: 3.15 Å3/Da / Density % sol: 61.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20% (w/v) PEG 8000, 0.1M CHAPS-NaOH (pH 10.5), 0.2M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 26458 / % possible obs: 98.6 % / Redundancy: 7 % / Net I/σ(I): 30.13 |
Reflection shell | Resolution: 2.45→2.54 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4f03 Resolution: 2.455→45.629 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.455→45.629 Å
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Refine LS restraints |
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LS refinement shell |
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