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Yorodumi- PDB-8bhz: The apo-crystal structure of a variant form of the 28-kDa Schisto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bhz | |||||||||
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Title | The apo-crystal structure of a variant form of the 28-kDa Schistosoma haematobium glutathione transferase in orthorhombic form | |||||||||
Components | Glutathione S-transferase class-mu 28 kDa isozyme | |||||||||
Keywords | TRANSFERASE / Glutathione S-transferases / Schistosoma haematobium / Schistosoma / haematobium / 28-kDa / Sh28GST / GST / orthorhombic | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Schistosoma haematobium (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Pandian, R. / Mfeka, S.M. / Onisuru, O. / Sayed, Y. / Achilonu, I.A. | |||||||||
Funding support | South Africa, 2items
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Citation | Journal: To Be Published Title: Biophysical and biochemical characterization of 28-kDa glutathione transferase from Schistosoma haematobium Authors: Mfeka, S.M. / Pandian, R. / Onisuru, O. / Sayed, Y. / Achilonu, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bhz.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bhz.ent.gz | 40.7 KB | Display | PDB format |
PDBx/mmJSON format | 8bhz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/8bhz ftp://data.pdbj.org/pub/pdb/validation_reports/bh/8bhz | HTTPS FTP |
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-Related structure data
Related structure data | 8alsS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23999.779 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma haematobium (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: P30114, glutathione transferase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density meas: 47.2 Mg/m3 / Density % sol: 46.55 % / Description: Long needle-shaped crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 15 mg/ml of Sh28GST in 100mM Tris-HCL at 7.5 pH with the crystallization condition consisting of 2.1 M ammonium sulfate, 100 mM Tris (pH 7.2), and 5 mM B-mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER IMUS 3.0 MICROFOCUS / Details: BRUKER IMUS DIAMOND MICROFOCUS / Wavelength: 1.5418 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Oct 25, 2022 / Details: Bruker PHOTON III 28 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→24.4 Å / Num. obs: 8867 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 21.42 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.084 / Rrim(I) all: 0.125 / Χ2: 0.97 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 859 / CC1/2: 0.802 / Rpim(I) all: 0.313 / Χ2: 1.02 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8ALS Resolution: 2.4→24.4 Å / SU ML: 0.297 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.8016 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: 25.71 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→24.4 Å
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Refine LS restraints |
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LS refinement shell |
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