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- PDB-4q3a: PylD cocrystallized with L-Lysine-Ne-3S-methyl-L-ornithine and NAD+ -
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Open data
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Basic information
Entry | Database: PDB / ID: 4q3a | ||||||
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Title | PylD cocrystallized with L-Lysine-Ne-3S-methyl-L-ornithine and NAD+ | ||||||
![]() | PYLD, pyrrolysine synthase | ||||||
![]() | OXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / Pyrrolysine | ||||||
Function / homology | ![]() Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Quitterer, F. / Beck, P. / Bacher, A. / Groll, M. | ||||||
![]() | ![]() Title: The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed by Pyrrolysine Synthase (PylD). Authors: Quitterer, F. / Beck, P. / Bacher, A. / Groll, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 422.5 KB | Display | ![]() |
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PDB format | ![]() | 348.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 44.2 KB | Display | |
Data in CIF | ![]() | 59.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4q39SC ![]() 4q3bC ![]() 4q3cC ![]() 4q3dC ![]() 4q3eC 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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6 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 27963.822 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q46E80, Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor |
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-Non-polymers , 9 types, 374 molecules ![](data/chem/img/NAI.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/2YC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/2YC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NAI / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-2YC / #6: Chemical | ChemComp-GOL / #7: Chemical | #8: Chemical | ChemComp-EDO / #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M TRIS, 27% PEG3350, 0.2 M NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2012 |
Radiation | Monochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. all: 57676 / Num. obs: 57408 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 3.1 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 4Q39 Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.584 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.247 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.118 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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