+Open data
-Basic information
Entry | Database: PDB / ID: 4q3e | ||||||
---|---|---|---|---|---|---|---|
Title | PylD cocrystallized with L-Ornithine-Nd-D-lysine and NAD+ | ||||||
Components | PYLD, pyrrolysine synthase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / Pyrrolysine | ||||||
Function / homology | Function and homology information 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 | Methanosarcina barkeri (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Quitterer, F. / Beck, P. / Bacher, A. / Groll, M. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4q3e.cif.gz | 213.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4q3e.ent.gz | 171.1 KB | Display | PDB format |
PDBx/mmJSON format | 4q3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/4q3e ftp://data.pdbj.org/pub/pdb/validation_reports/q3/4q3e | HTTPS FTP |
---|
-Related structure data
Related structure data | 4q39SC 4q3aC 4q3bC 4q3cC 4q3dC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
| ||||||||||||
Details | two molecules in the AU |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27963.822 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina barkeri (archaea) / Strain: Fusaro / Gene: Mbar_A0835 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q46E80, Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor |
---|
-Non-polymers , 8 types, 205 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-SO4 / | #8: Chemical | ChemComp-GOL / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.41 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2013 |
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→20 Å / Num. all: 33346 / Num. obs: 33310 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4Q39 Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 10 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.211 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 47.372 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|