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Yorodumi- PDB-7esg: Crystal structure of Haloarcula marismortui CheB with Glutathione... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7esg | ||||||
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Title | Crystal structure of Haloarcula marismortui CheB with Glutathione S-transferase expression tag | ||||||
Components | Glutathione S-transferase,Protein-glutamate methylesterase/protein-glutamine glutaminase | ||||||
Keywords | TRANSFERASE / HYDROLASE / CheB methylesterase | ||||||
Function / homology | Function and homology information protein-glutamate methylesterase / protein-glutamate methylesterase activity / protein deamination / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein demethylation / phosphorelay response regulator activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process ...protein-glutamate methylesterase / protein-glutamate methylesterase activity / protein deamination / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein demethylation / phosphorelay response regulator activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / chemotaxis / cytoplasm Similarity search - Function | ||||||
Biological species | Schistosoma japonicum (invertebrata) Haloarcula marismortui (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å | ||||||
Authors | Chen, K.L. / Yang, C.S. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of Haloarcula marismortui CheB with Glutathione S-transferase expression tag Authors: Chen, K.L. / Yang, C.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7esg.cif.gz | 149.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7esg.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 7esg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7esg_validation.pdf.gz | 435.4 KB | Display | wwPDB validaton report |
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Full document | 7esg_full_validation.pdf.gz | 497.5 KB | Display | |
Data in XML | 7esg_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 7esg_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/7esg ftp://data.pdbj.org/pub/pdb/validation_reports/es/7esg | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 65411.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma japonicum (invertebrata), (gene. exp.) Haloarcula marismortui (Halophile) Gene: cheB / Production host: Escherichia coli (E. coli) / References: UniProt: P08515, UniProt: Q5V0B3 |
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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: 1.95 Å3/Da / Density % sol: 36.96 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 20% PEG 3350, 200 mM Potassium citrate tribasic monohydrate, pH 8.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→30 Å / Num. obs: 17534 / % possible obs: 99.51 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.29 Å2 / Rrim(I) all: 0.097 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.53→2.62 Å / Num. unique obs: 1638 / Rrim(I) all: 0.443 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: robetta model Resolution: 2.53→23.86 Å / Cross valid method: FREE R-VALUE / σ(F): 38.73 / Phase error: 39.0117 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.53→23.86 Å
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Refine LS restraints |
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LS refinement shell |
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