+Open data
-Basic information
Entry | Database: PDB / ID: 8hm5 | ||||||
---|---|---|---|---|---|---|---|
Title | Epoxide hydrolase from Caballeronia sordidicola PAMC 26510 | ||||||
Components | Epoxide hydrolase | ||||||
Keywords | HYDROLASE / Bacterial epoxide hydrolase | ||||||
Function / homology | Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Epoxide hydrolase Function and homology information | ||||||
Biological species | Caballeronia sordidicola (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | ||||||
Authors | Hwang, J. / Lee, M.J. / Do, H. / Lee, J.H. | ||||||
Funding support | Korea, Republic Of, 1items
| ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2024 Title: Structural insights into the distinct substrate preferences of two bacterial epoxide hydrolases. Authors: Hwang, J. / Lee, M.J. / Lee, S.G. / Do, H. / Lee, J.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8hm5.cif.gz | 137.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8hm5.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 8hm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hm5_validation.pdf.gz | 429.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8hm5_full_validation.pdf.gz | 433.3 KB | Display | |
Data in XML | 8hm5_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 8hm5_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/8hm5 ftp://data.pdbj.org/pub/pdb/validation_reports/hm/8hm5 | HTTPS FTP |
-Related structure data
Related structure data | 8hguC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35706.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caballeronia sordidicola (bacteria) / Gene: PAMC26510_32755 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A242M8J4 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.43 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium formate and 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 113 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 5, 2020 |
Radiation | Monochromator: Confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→81.21 Å / Num. obs: 20365 / % possible obs: 97.7 % / Redundancy: 4.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.43→2.56 Å / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 2022 / CC1/2: 0.968 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→43.41 Å / SU ML: 0.2255 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.5241 / Stereochemistry target values: CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.43→43.41 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|