+
Open data
-
Basic information
Entry | Database: PDB / ID: 6z68 | ||||||
---|---|---|---|---|---|---|---|
Title | A novel metagenomic alpha/beta-fold esterase | ||||||
![]() | Acetyl esterase/lipase | ||||||
![]() | HYDROLASE / alpha/beta-fold hydrolase / esterase / metagenome / inhibitor-bound / substrate promiscuity | ||||||
Function / homology | Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / DI(HYDROXYETHYL)ETHER / Acetyl esterase/lipase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bollinger, A. / Thies, S. / Hoeppner, A. / Kobus, S. / Jaeger, K.-E. / Smits, S.H.J. | ||||||
![]() | ![]() Title: Crystal structures of a novel family IV esterase in free and substrate-bound form. Authors: Hoppner, A. / Bollinger, A. / Kobus, S. / Thies, S. / Coscolin, C. / Ferrer, M. / Jaeger, K.E. / Smits, S.H.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 323.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 262.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 449 KB | Display | |
Data in XML | ![]() | 37.1 KB | Display | |
Data in CIF | ![]() | 58 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 40513.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.87 % |
---|---|
Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop Details: 0.25 M magnesium chloride, 0.1 M Tris pH 8.5 and 35 % (w/v) PEG 4000 with 0.01 M TCEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976246 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→55.28 Å / Num. obs: 155980 / % possible obs: 96.69 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.64 |
Reflection shell | Resolution: 1.353→1.402 Å / Rmerge(I) obs: 0.488 / Num. unique obs: 10966 / CC1/2: 0.804 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: xxxx Resolution: 1.35→55.28 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.086 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.09 Å2 / Biso mean: 18.011 Å2 / Biso min: 7.23 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→55.28 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.353→1.388 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|