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- PDB-2cye: Crystal structure of Thioesterase complexed with coenzyme A and Z... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2cye | ||||||
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Title | Crystal structure of Thioesterase complexed with coenzyme A and Zn from Thermus thermophilus HB8 | ||||||
![]() | Putative thioesterase | ||||||
![]() | HYDROLASE / Structural Genomics / esterase / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / COENZYME A / Putative thioesterase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hosaka, T. / Kato-Murayama, M. / Murayama, K. / Kishishita, S. / Handa, N. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Structure of the putative thioesterase protein TTHA1846 from Thermus thermophilus HB8 complexed with coenzyme A and a zinc ion. Authors: Hosaka, T. / Murayama, K. / Kato-Murayama, M. / Urushibata, A. / Akasaka, R. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.2 KB | Display | ![]() |
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PDB format | ![]() | 102.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 27.7 KB | Display | |
Data in CIF | ![]() | 37.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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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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3 |
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Unit cell |
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Details | In this crystal packing, it looks like dimer. But, there is no experimental evidence. |
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Components
#1: Protein | Mass: 15273.065 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q5SH84, Hydrolases; Acting on ester bonds; Thioester hydrolases #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-COA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M Acetate, 0.8M ammonium sulphate, 3% PEG400, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: May 18, 2005 / Details: mirrors | ||||||||||||
Radiation | Monochromator: silicon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. obs: 41903 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.9423 % / Biso Wilson estimate: 6.4 Å2 / Rsym value: 0.089 / Net I/σ(I): 13.3748 | ||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 4.1454 / Rsym value: 0.286 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.284 Å2 / ksol: 0.381167 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→47.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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