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Open data
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Basic information
Entry | Database: PDB / ID: 5gzm | ||||||
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Title | Cyclodeaminase_PA | ||||||
![]() | Lysine cyclodeaminase | ||||||
![]() | LYASE / dimer / complex / cyclization / deamination | ||||||
Function / homology | ![]() ornithine cyclodeaminase activity / ornithine cyclodeaminase / thyroid hormone metabolic process / thyroid hormone binding / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Ying, H. / Chen, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cyclodeaminase_PA Authors: Ying, H. / Chen, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151 KB | Display | ![]() |
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PDB format | ![]() | 118.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38106.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pipA, SPRI_0308, SPRI_7045 / Plasmid: pET-28a / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2% (v/v) Polyethylene glycol 400, 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 63049 / % possible obs: 96.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 26.02 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.01 |
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Processing
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Refinement | Resolution: 1.8→37.79 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.644 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.115 / 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: 34.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→37.79 Å
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