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Open data
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Basic information
Entry | Database: PDB / ID: 8dl5 | ||||||
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Title | Crystal structure of PLP-dependent Mannich cyclase LolT | ||||||
![]() | Aminotransferase, class V/Cysteine desulfurase | ||||||
![]() | BIOSYNTHETIC PROTEIN / PLP-dependent C-C bond forming Cyclase | ||||||
Function / homology | Aminotransferase class V domain / Aminotransferase class-V / transaminase activity / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Aminotransferase, class V/Cysteine desulfurase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gao, J. / Hai, Y. | ||||||
Funding support | 1items
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![]() | ![]() Title: A pyridoxal 5'-phosphate-dependent Mannich cyclase. Authors: Gao, J. / Liu, S. / Zhou, C. / Lara, D. / Zou, Y. / Hai, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.6 KB | Display | ![]() |
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PDB format | ![]() | 139.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 730.4 KB | Display | ![]() |
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Full document | ![]() | 741.8 KB | Display | |
Data in XML | ![]() | 32.3 KB | Display | |
Data in CIF | ![]() | 44.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 55579.215 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: 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: 2.46 Å3/Da / Density % sol: 50.05 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium malonate, pH 5.18, 14% w/v PEG3350 |
-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 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 62480 / % possible obs: 100 % / Redundancy: 18.8 % / Biso Wilson estimate: 37.92 Å2 / CC1/2: 0.974 / CC star: 0.993 / Rpim(I) all: 0.042 / Net I/σ(I): 27.22 |
Reflection shell | Resolution: 2.11→2.15 Å / Redundancy: 16.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3034 / CC1/2: 0.713 / CC star: 0.912 / Rpim(I) all: 0.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Alphafold2 predicted model Resolution: 2.1→37.66 Å / SU ML: 0.2878 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3501 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 43.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→37.66 Å
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Refine LS restraints |
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LS refinement shell |
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