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Open data
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Basic information
Entry | Database: PDB / ID: 3cl6 | ||||||
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Title | Crystal structure of Puue Allantoinase | ||||||
![]() | Puue allantoinase | ||||||
![]() | HYDROLASE / Allantoin / Uric acid / nitrogen fixation | ||||||
Function / homology | ![]() hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramazzina, I. / Cendron, L. / Folli, C. / Berni, R. / Monteverdi, D. / Zanotti, G. / Percudani, R. | ||||||
![]() | ![]() Title: Logical identification of an allantoinase analog (puuE) recruited from polysaccharide deacetylases Authors: Ramazzina, I. / Cendron, L. / Folli, C. / Berni, R. / Monteverdi, D. / Zanotti, G. / Percudani, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.9 KB | Display | ![]() |
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PDB format | ![]() | 107.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.2 KB | Display | ![]() |
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Full document | ![]() | 442.5 KB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cl7C ![]() 3cl8C ![]() 1z7aS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 35468.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | THIS SEQUENCE HAS BEEN DEPOSITED IN GENEBANK, WITH ACCESSION CODE EU293536, AND IT WILL BE LOCATED ...THIS SEQUENCE HAS BEEN DEPOSITED IN GENEBANK, WITH ACCESSION CODE EU293536, AND IT WILL BE LOCATED IN UNIPROTKB LATER. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 0.2M (NH4)2SO4, 0.1M NaCacodylate, pH 6.5, 30% PEG 8000, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2007 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→52.71 Å / Num. all: 81449 / Num. obs: 81449 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.58→1.67 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 1.7 / Num. unique all: 11879 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Z7A Resolution: 1.58→9.98 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.911 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.102 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; ARG 167 side chain is in alternate conformations
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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: 13.649 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→9.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.62 Å / Total num. of bins used: 20
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