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Yorodumi- PDB-8als: The apo-crystal structure of a variant form of the 28-kDa Schisto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8als | |||||||||
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Title | The apo-crystal structure of a variant form of the 28-kDa Schistosoma haematobium glutathione transferase | |||||||||
Components | (Glutathione S-transferase class-mu 28 kDa isozyme) x 2 | |||||||||
Keywords | TRANSFERASE / Glutathione S-transferases / Schistosoma haematobium / Schistosoma / haematobium / 28-kDa / Sh28GST / GST | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Schistosoma haematobium (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Pandian, R. / Makumbe, H.H. / Sayed, Y. / Achilonu, I.A. | |||||||||
Funding support | South Africa, 2items
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Citation | Journal: To Be Published Title: The apo-crystal structure of a variant form of the 28-kDa Schistosoma haematobium glutathione transferase Authors: Makumbe, H.H. / Pandian, R. / 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 | 8als.cif.gz | 107.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8als.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 8als.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/8als ftp://data.pdbj.org/pub/pdb/validation_reports/al/8als | HTTPS FTP |
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-Related structure data
Related structure data | 1oe8S 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: 23293.953 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: Protein | Mass: 23351.004 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 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.98 % / Description: Long needle-shaped crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 5.3 mg/ml of Sh28GST in 25mM of sodium phosphate buffer (NaH2PO4) at 7.5 pH with the crystallization condition consisting of 2.1 M ammonium sulfate, 100 mM Tris (pH 7.5), 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 / Wavelength: 1.5418 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: May 18, 2022 |
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: 2.3→24.68 Å / Num. obs: 19612 / % possible obs: 98.8 % / Redundancy: 8.1 % / Biso Wilson estimate: 15.21 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1752 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OE8 Resolution: 2.3→24.678 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→24.678 Å
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Refine LS restraints |
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LS refinement shell |
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