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- PDB-5v12: Crystal structure of Carbon Sulfoxide lyase, Egt2 Y134F with sulf... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5v12 | ||||||||||||
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Title | Crystal structure of Carbon Sulfoxide lyase, Egt2 Y134F with sulfenic acid intermediate | ||||||||||||
![]() | (Hercynylcysteine sulfoxide lyase) x 2 | ||||||||||||
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Function / homology | ![]() hercynylcysteine sulfoxide lyase activity (ergothioneine-forming) / ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Irani, S. / Zhang, Y. | ||||||||||||
![]() | ![]() Title: Snapshots of C-S Cleavage in Egt2 Reveals Substrate Specificity and Reaction Mechanism. Authors: Irani, S. / Naowarojna, N. / Tang, Y. / Kathuria, K.R. / Wang, S. / Dhembi, A. / Lee, N. / Yan, W. / Lyu, H. / Costello, C.E. / Liu, P. / Zhang, Y.J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 696.5 KB | Display | ![]() |
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PDB format | ![]() | 570.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5utsSC ![]() 5v1xC S: Starting model for refinement C: citing same article ( |
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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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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | Dimer as determined by gel filtration |
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Components
#1: Protein | Mass: 56426.262 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987 Gene: egt-2, NCU11365 / Production host: ![]() ![]() ![]() ![]() #2: Protein | | Mass: 56513.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987 Gene: egt-2, NCU11365 / Production host: ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-FMT / ![]() #4: Chemical | #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.33 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 30% PEG 3350, 50mM HEPES pH 7.5, 200mM sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.45→50 Å / Num. obs: 146021 / % possible obs: 91.2 % / Redundancy: 2.9 % / Net I/σ(I): 8.46 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5UTS Resolution: 2.451→49.577 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.451→49.577 Å
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Refine LS restraints |
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LS refinement shell |
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