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Yorodumi- PDB-5v12: Crystal structure of Carbon Sulfoxide lyase, Egt2 Y134F with sulf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v12 | ||||||||||||
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Title | Crystal structure of Carbon Sulfoxide lyase, Egt2 Y134F with sulfenic acid intermediate | ||||||||||||
Components | (Hercynylcysteine sulfoxide lyase) x 2 | ||||||||||||
Keywords | LYASE / C-S lyase / PLP dependent | ||||||||||||
Function / homology | Function and homology information Lyases; Carbon-sulfur lyases / hercynylcysteine sulfoxide lyase activity (ergothioneine-forming) / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Neurospora crassa OR74A (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.451 Å | ||||||||||||
Authors | Irani, S. / Zhang, Y. | ||||||||||||
Citation | Journal: Cell Chem Biol / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v12.cif.gz | 696.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v12.ent.gz | 570.6 KB | Display | PDB format |
PDBx/mmJSON format | 5v12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v12_validation.pdf.gz | 565.3 KB | Display | wwPDB validaton report |
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Full document | 5v12_full_validation.pdf.gz | 618.5 KB | Display | |
Data in XML | 5v12_validation.xml.gz | 126 KB | Display | |
Data in CIF | 5v12_validation.cif.gz | 167.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/5v12 ftp://data.pdbj.org/pub/pdb/validation_reports/v1/5v12 | HTTPS FTP |
-Related structure data
Related structure data | 5utsSC 5v1xC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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 |
-Components
#1: Protein | Mass: 56426.262 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neurospora crassa OR74A (fungus) Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987 Gene: egt-2, NCU11365 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A7UX13, Lyases; Carbon-sulfur lyases #2: Protein | | Mass: 56513.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neurospora crassa OR74A (fungus) Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987 Gene: egt-2, NCU11365 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A7UX13, Lyases; Carbon-sulfur lyases #3: Chemical | ChemComp-FMT / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
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: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 146021 / % possible obs: 91.2 % / Redundancy: 2.9 % / Net I/σ(I): 8.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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