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- PDB-4yzo: Crystal Structure Analysis of Thiolase-like protein, ST0096 from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yzo | ||||||
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Title | Crystal Structure Analysis of Thiolase-like protein, ST0096 from Sulfolobus Tokodaii | ||||||
![]() | Putative acyl-CoA acyltransferase | ||||||
![]() | TRANSFERASE / lipid metabolism / thiolase-like fold | ||||||
Function / homology | ![]() acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Padmanabhan, B. / Manjula, R. / Yokoyama, S. / Bessho, Y. | ||||||
![]() | ![]() Title: Crystal Structure Analysis of Thiolase-like protein, ST0096 from Sulfolobus Tokodaii Authors: Padmanabhan, B. / Manjula, R. / Yokoyama, S. / Bessho, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 313.4 KB | Display | ![]() |
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PDB format | ![]() | 263.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 493.7 KB | Display | ![]() |
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Full document | ![]() | 508.8 KB | Display | |
Data in XML | ![]() | 66.9 KB | Display | |
Data in CIF | ![]() | 100.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 40914.414 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q976U3, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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-Non-polymers , 5 types, 1523 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-IMD / | #4: Chemical | ChemComp-ACT / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.29 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 8 Details: 30 % 2-ethoxyethanol, 50 mM Calcium Acetate, 0.1 M Imidazole, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 120 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 2, 2007 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.65→50 Å / Num. obs: 180973 / % possible obs: 96.7 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 16.7 | ||||||||||||
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.8 / % possible all: 78.3 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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: 23.83 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→19.99 Å
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Refine LS restraints |
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