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Yorodumi- PDB-5yu1: Structural basis for recognition of L-lysine, L-ornithine, and L-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yu1 | ||||||
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Title | Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase | ||||||
Components | Lysine cyclodeaminase | ||||||
Keywords | LYASE / L-lysine cyclodeaminase / Streptomyces pristinaespiralis | ||||||
Function / homology | ornithine cyclodeaminase / ornithine cyclodeaminase activity / Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / (2S)-piperidine-2-carboxylic acid / Lysine cyclodeaminase Function and homology information | ||||||
Biological species | Streptomyces pristinaespiralis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.923 Å | ||||||
Authors | Min, K.J. / Yoon, H.J. / Matsuura, A. / Kim, Y.H. / Lee, H.H. | ||||||
Citation | Journal: Mol. Cells / Year: 2018 Title: Structural Basis for Recognition of L-lysine, L-ornithine, and L-2,4-diamino Butyric Acid by Lysine Cyclodeaminase. Authors: Min, K. / Yoon, H.J. / Matsuura, A. / Kim, Y.H. / Lee, H.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yu1.cif.gz | 295.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yu1.ent.gz | 240.1 KB | Display | PDB format |
PDBx/mmJSON format | 5yu1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/5yu1 ftp://data.pdbj.org/pub/pdb/validation_reports/yu/5yu1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36587.363 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces pristinaespiralis (bacteria) Gene: pipA, SPRI_0308, SPRI_7045 / Production host: Escherichia coli (E. coli) / References: UniProt: D9UBW0, ornithine cyclodeaminase #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-YCP / ( #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 100mM CAPSO buffer (pH 9.6), 0.2M Li2SO4, 0.9M Na-K tartrate, 2% polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→50 Å / Num. obs: 134717 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 39.6 |
Reflection shell | Resolution: 1.92→1.95 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 12 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Resolution: 1.923→31.416 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 18.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.923→31.416 Å
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Refine LS restraints |
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LS refinement shell |
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