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Open data
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Basic information
Entry | Database: PDB / ID: 8yfy | ||||||
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Title | CRYSTAL STRUCTURE OF THE EST1 H274D MUTANT AT PH 4.2 | ||||||
![]() | Carboxylesterase | ||||||
![]() | HYDROLASE / ALPHA/BETA-HYDRORASE FOLD / CARBOXYLESTERASE | ||||||
Function / homology | Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / : / carboxylesterase / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / Carboxylesterase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Unno, H. / Oshima, Y. / Nishino, T. / Nakayama, T. / Kusunoki, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Lowering pH optimum of activity of SshEstI, a slightly alkaliphilic archaeal esterase of the hormone-sensitive lipase family. Authors: Ohara, K. / Oshima, Y. / Unno, H. / Nagano, S. / Kusunoki, M. / Takahashi, S. / Waki, T. / Yamashita, S. / Nakayama, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.6 KB | Display | ![]() |
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PDB format | ![]() | 56.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 646.4 KB | Display | ![]() |
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Full document | ![]() | 648.6 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8yfzC ![]() 1wzj ![]() 1wzp ![]() 1wzq ![]() 1wzr ![]() 1wzs C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 33528.344 Da / Num. of mol.: 1 / Mutation: H274D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Sugar | ChemComp-BOG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 42.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.2 Details: 12% PEG 3000, 200 MM NACL, 100 MM PHOSPHATE-CITRATE, PH 4.2, VAPOR DIFFUSION, TEMPERATURE 293K PH range: 4.2 |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: Bruker DIP-6040 / Detector: IMAGE PLATE / Date: Sep 22, 2003 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→18.7 Å / Num. obs: 46275 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 18.15 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 46275 / % possible all: 78.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.65 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→18.7 Å
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Refine LS restraints |
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