+
Open data
-
Basic information
Entry | Database: PDB / ID: 7yvt | ||||||
---|---|---|---|---|---|---|---|
Title | S-formylglutathione hydrolase from Variovorax sp. PAMC 28711 | ||||||
![]() | S-formylglutathione hydrolase | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hwang, J. / Do, H. / Lee, J.H. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural basis for the substrate specificity of an S-formylglutathione hydrolase derived from Variovorax sp. PAMC 28711. Authors: Hwang, J. / Kim, B. / Lee, M.J. / Nam, Y. / Youn, U.J. / Lee, C.S. / Oh, T.J. / Park, H.H. / Do, H. / Lee, J.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 189 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 137.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 466.2 KB | Display | |
Data in XML | ![]() | 34.1 KB | Display | |
Data in CIF | ![]() | 48.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fcxS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
3 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 32098.539 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Chain A : Residues, Met1 at N-terminal and Gly286 to Pro295 at C-terminal, are missing. Chain B : Residues from Gly286 to Pro295 at C-terminal are missing. Chain C : Residues, Met1 to Asp3 ...Details: Chain A : Residues, Met1 at N-terminal and Gly286 to Pro295 at C-terminal, are missing. Chain B : Residues from Gly286 to Pro295 at C-terminal are missing. Chain C : Residues, Met1 to Asp3 at N-terminal and Asn284 to Pro295 at C-terminal, are missing. Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A126ZFJ3, S-formylglutathione hydrolase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.7 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M sodium chloride, 0.1 M Bis-Tris:HCl (pH 6.5), and 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→50 Å / Num. obs: 31349 / % possible obs: 95.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 36.28 Å2 / CC1/2: 0.968 / Net I/σ(I): 20.096 |
Reflection shell | Resolution: 2.38→2.42 Å / Num. unique obs: 1671 / CC1/2: 0.932 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3FCX Resolution: 2.38→43.66 Å / SU ML: 0.2716 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.484 / 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: 43.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→43.66 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|