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- PDB-4ord: Crystal Structure of Zebra Fish Thioesterase Superfamily Member 2 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ord | ||||||
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Title | Crystal Structure of Zebra Fish Thioesterase Superfamily Member 2 | ||||||
![]() | Thioesterase Superfamily Member 2 | ||||||
![]() | HYDROLASE / Hotdog / thioesterase / Acyl-CoA | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yu, S.S. / Li, H. / Gao, F. / Xu, H. / Gong, W.M. | ||||||
![]() | ![]() Title: Crystal Structure and Potential Physiological Role of Zebra Fish Thioesterase Superfamily Member 2 (fTHEM2) Authors: Yu, S.S. / Li, H. / Gao, F. / Wang, Y. / Miao, L.Y. / Zhang, J. / Xu, H. / Gong, W.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.4 KB | Display | ![]() |
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PDB format | ![]() | 177.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2f0xS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 16152.664 Da / Num. of mol.: 4 / Fragment: UNP residues 6-146 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: F6P1Y9, Hydrolases; Acting on ester bonds; Thioester hydrolases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.44 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Ammonium Acetate, 0.1M Bis-Tris, 17%(w/v) PEG10000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 10, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9716 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 50707 / Num. obs: 50707 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2F0X Resolution: 1.8→35.02 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.085 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.136 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.401 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→35.02 Å
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Refine LS restraints |
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