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- PDB-8ffu: Structure of GntC, a PLP-dependent enzyme catalyzing L-enduracidi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ffu | ||||||
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Title | Structure of GntC, a PLP-dependent enzyme catalyzing L-enduracididine biosynthesis from (S)-4-hydroxy-L-arginine, with the substrate bound | ||||||
![]() | (Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme) x 2 | ||||||
![]() | BIOSYNTHETIC PROTEIN / PLP / GntC / cyclodehydration / (S)-4-hydroxy-L-arginine / guanitoxin / L-enduracididine / cyanobacterial blooms / biocatalysis / biosynthesis / cyanobacterium | ||||||
Function / homology | ![]() transaminase activity / biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, P.Y.-T. / Moore, B.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanistic and Structural Insights into a Divergent PLP-Dependent l-Enduracididine Cyclase from a Toxic Cyanobacterium. Authors: Cordoza, J.L. / Chen, P.Y. / Blaustein, L.R. / Lima, S.T. / Fiore, M.F. / Chekan, J.R. / Moore, B.S. / McKinnie, S.M.K. #1: Journal: Biorxiv / Year: 2023 Title: Mechanistic and structural insights into a divergent PLP-dependent L-enduracididine cyclase from a toxic cyanobacterium. Authors: Cordoza, J.L. / Chen, P.Y. / Blaustein, L.R. / Lima, S.T. / Fiore, M.F. / Chekan, J.R. / Moore, B.S. / McKinnie, S.M.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 | ![]() | 357.1 KB | Display | ![]() |
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PDB format | ![]() | 231.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 49.6 KB | Display | |
Data in CIF | ![]() | 67.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fftSC S: Starting model for refinement C: citing same article ( |
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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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41637.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 41865.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.32 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop Details: 24-27% (w/v) PEG 3350, 0.40-0.44 M MgCl2, 0.10 M Tris pH 8.5, 1 mM PLP, and 10 mM S-4-hydroxy-L-Arg |
-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 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→100 Å / Num. obs: 87584 / % possible obs: 98.6 % / Redundancy: 5.8 % / Rsym value: 0.094 / Net I/σ(I): 13.56 |
Reflection shell | Resolution: 2.04→2.16 Å / Num. unique obs: 14110 / CC1/2: 0.705 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8FFT Resolution: 2.04→36.8 Å / Cross valid method: FREE R-VALUE / σ(F): 95.95 / Phase error: 24.4897 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→36.8 Å
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Refine LS restraints |
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LS refinement shell |
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