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Open data
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Basic information
Entry | Database: PDB / ID: 4j4b | ||||||
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Title | PylD in complex with L-lysine-Ne-D-ornithine and NADH | ||||||
![]() | PylD | ||||||
![]() | OXIDOREDUCTASE / Pyrrolysine / 22nd Amino Acid / Biosynthesis / Rossmann Fold / Dehydrogenase / NADH | ||||||
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: Structure and Reaction Mechanism of 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 | ![]() | 221.2 KB | Display | ![]() |
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PDB format | ![]() | 179 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27876.744 Da / Num. of mol.: 2 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 , 5 types, 215 molecules ![](data/chem/img/NAI.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/0TF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
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![](data/chem/img/0TF.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.66 % |
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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 Li2SO4, 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: Bruker Platinum 135 / Detector: CCD / Date: Dec 16, 2012 |
Radiation | Monochromator: BRUKER MICROSTAR MICRO-FOCUS (MONTEL OPTICS) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→60 Å / Num. all: 46157 / Num. obs: 46111 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.4 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: SeMet-model; coordinates have not been deposited Resolution: 1.9→10 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.472 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 35.879 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.948 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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