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- PDB-5uxg: Protein 84 with aldehyde deformylating oxygenase activity from Su... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uxg | ||||||
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Title | Protein 84 with aldehyde deformylating oxygenase activity from Sulfolobus tokodaii (monoclinic) | ||||||
![]() | aldehyde deformylating oxygenase | ||||||
![]() | LYASE / decarbonylase / iron / ferritin | ||||||
Function / homology | Ribonucleotide reductase-like / Ferritin-like superfamily / oxidoreductase activity / PHOSPHATE ION / Ferritin-like domain-containing protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wilson, D.K. / Mak, W.S. / Siegel, J.B. | ||||||
![]() | ![]() Title: Protein 84 with aldehyde deformylating oxygenase activity from Sulfolobus tokodaii (monoclinic) Authors: Wilson, D.K. / Mak, W.S. / Siegel, J.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.4 KB | Display | ![]() |
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PDB format | ![]() | 78.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25917.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: ST1620, STK_16200 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Potassium phosphate, PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→63.61 Å / Num. obs: 55207 / % possible obs: 96.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.72→1.75 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.7 / % possible all: 57 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: theoretical Resolution: 1.72→63.61 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.494 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.106 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.536 Å2
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Refinement step | Cycle: 1 / Resolution: 1.72→63.61 Å
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Refine LS restraints |
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