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Open data
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Basic information
Entry | Database: PDB / ID: 7yvy | ||||||
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Title | Crystal structure of thiolase PFC_04095 from Pyrococcus furiosus | ||||||
![]() | Acetyl-CoA acetyltransferase | ||||||
![]() | TRANSFERASE / Pyrococcus furiosus / acetoacetyl-CoA thiolase / acetyl-CoA acetyltransferase | ||||||
Function / homology | acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like / Acetyl-CoA acetyltransferase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Singh, R. / Das, A.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of thiolase PFC_04095 from Pyrococcus furiosus Authors: Singh, R. / Das, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 391 KB | Display | ![]() |
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PDB format | ![]() | 324.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6esqS S: Starting model for refinement |
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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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41019.887 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M carboxylic acids, 0.1 M buffer system 3 pH 8.5 and 50 % v/v precipitant mix 4. Carboxylic acids: 0.2 M each of sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, ...Details: 0.1 M carboxylic acids, 0.1 M buffer system 3 pH 8.5 and 50 % v/v precipitant mix 4. Carboxylic acids: 0.2 M each of sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium potassium tartrate tetrahydrate and sodium oxamate. Buffer system 3: Tris (base); bicine pH 8.5 Precipitant mix 4: MPD_PIK_P3350 (25 % v/v MPD, 25 % PEG 1000, 25 % w/v PEG 3350) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→48.03 Å / Num. obs: 36797 / % possible obs: 99.24 % / Redundancy: 6.7 % / Biso Wilson estimate: 77.7 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 16.93 |
Reflection shell | Resolution: 2.7→2.797 Å / Num. unique obs: 3666 / CC1/2: 0.923 / CC star: 0.98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ESQ Resolution: 2.7→48.03 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 176.95 Å2 / Biso mean: 91.3016 Å2 / Biso min: 43.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→48.03 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Origin x: 25.671 Å / Origin y: -33.553 Å / Origin z: -7.7945 Å
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Refinement TLS group |
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