+Open data
-Basic information
Entry | Database: PDB / ID: 4jk3 | ||||||
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Title | PylD holoenzyme (SeMet) | ||||||
Components | PylD | ||||||
Keywords | OXIDOREDUCTASE / Pyrrolysine / 22nd Amino Acid / Biosynthesis / Rossmann Fold / Dehydrogenase / NAD | ||||||
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 / SAD / Resolution: 2.5 Å | ||||||
Authors | Quitterer, F. / Beck, P. / Bacher, A. / Groll, M. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jk3.cif.gz | 202.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jk3.ent.gz | 172.7 KB | Display | PDB format |
PDBx/mmJSON format | 4jk3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jk3_validation.pdf.gz | 941.2 KB | Display | wwPDB validaton report |
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Full document | 4jk3_full_validation.pdf.gz | 952.4 KB | Display | |
Data in XML | 4jk3_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 4jk3_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/4jk3 ftp://data.pdbj.org/pub/pdb/validation_reports/jk/4jk3 | HTTPS FTP |
-Related structure data
-Links
-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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 28158.113 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 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.43 % |
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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 source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9798 Å |
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Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 3, 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: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.5→2.6 Å / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 21.626 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 1.033 / ESU R Free: 0.315 / 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: 54.408 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.563 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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