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Open data
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Basic information
Entry | Database: PDB / ID: 5gzi | ||||||
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Title | Cyclodeaminase_PA | ||||||
![]() | Lysine cyclodeaminase | ||||||
![]() | LYASE / dimer / complex / cyclization / deamination | ||||||
Function / homology | ![]() ornithine cyclodeaminase / ornithine cyclodeaminase activity / 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 | ![]() | 148.7 KB | Display | ![]() |
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PDB format | ![]() | 117.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Data in CIF | ![]() | 41.8 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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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: 48.63 % |
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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: Aug 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→50 Å / Num. obs: 37354 / % possible obs: 99.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.53 |
Reflection shell | Resolution: 2.17→2.21 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.62 / % possible all: 99.8 |
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Processing
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Refinement | Resolution: 2.17→47.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.716 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.2 / 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: 35.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.17→47.84 Å
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Refine LS restraints |
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