+Open data
-Basic information
Entry | Database: PDB / ID: 8ilj | ||||||
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Title | S-formylglutathione hydrolase (BuSFGH) from Burkholderiaceae sp. | ||||||
Components | S-formylglutathione hydrolase | ||||||
Keywords | HYDROLASE / S-formylglutathione hydrolase | ||||||
Function / homology | S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / S-formylglutathione hydrolase / formaldehyde catabolic process / Esterase-like / Putative esterase / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / S-formylglutathione hydrolase Function and homology information | ||||||
Biological species | Burkholderiaceae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Hwang, J. / Lee, J.H. / Do, H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Crystals / Year: 2023 Title: Crystal structure and functional characterization of an S-formylglutathione hydrolase (BuSFGH) from Burkholderiaceae sp. Authors: Hwang, J. / Do, H. / Shim, Y.S. / Lee, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ilj.cif.gz | 128.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ilj.ent.gz | 97.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ilj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/8ilj ftp://data.pdbj.org/pub/pdb/validation_reports/il/8ilj | HTTPS FTP |
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-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: 30839.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderiaceae (bacteria) / Gene: PAMC26510_23250 / Production host: Escherichia coli (E. coli) References: UniProt: A0A242MJ43, S-formylglutathione hydrolase #2: 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: 2.51 Å3/Da / Density % sol: 51.05 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium citrate pH 5.0 and 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→29.52 Å / Num. obs: 65529 / % possible obs: 99.7 % / Redundancy: 12.5 % / Biso Wilson estimate: 19.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08096 / Net I/σ(I): 20.63 |
Reflection shell | Resolution: 1.73→1.76 Å / Rmerge(I) obs: 0.3969 / Num. unique obs: 6421 / CC1/2: 0.969 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→29.52 Å / SU ML: 0.1876 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.8011 / Stereochemistry target values: 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: 20.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→29.52 Å
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Refine LS restraints |
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LS refinement shell |
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