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Open data
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Basic information
Entry | Database: PDB / ID: 2o73 | ||||||
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Title | Structure of OHCU decarboxylase in complex with allantoin | ||||||
![]() | OHCU decarboxylase | ||||||
![]() | LYASE / Decarboxylation / OHCU / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline / HIU / 5-hydroxyisourate | ||||||
Function / homology | ![]() 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / allantoin metabolic process / urate catabolic process / purine nucleobase metabolic process / peroxisome Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cendron, L. / Berni, R. / Folli, C. / Ramazzina, I. / Percudani, R. / Zanotti, G. | ||||||
![]() | ![]() Title: The structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase provides insights into the mechanism of uric acid degradation. Authors: Cendron, L. / Berni, R. / Folli, C. / Ramazzina, I. / Percudani, R. / Zanotti, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 214 KB | Display | ![]() |
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PDB format | ![]() | 172.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.3 KB | Display | ![]() |
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Full document | ![]() | 500.9 KB | Display | |
Data in XML | ![]() | 43.4 KB | Display | |
Data in CIF | ![]() | 60.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2o70SC ![]() 2o74C 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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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 2 - 164 / Label seq-ID: 2 - 164
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Details | The enzyme in solution is a dimer, there are three dimers in the asymmetric unit (AB, CD, EF) |
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Components
#1: Protein | Mass: 19768.645 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-2AL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.41 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion / pH: 8.5 Details: 20% (v/v) EtOH, 100mM TrisHCl, pH 8.5, VAPOR DIFFUSION, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 29, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→88.39 Å / Num. all: 104588 / Num. obs: 104588 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.7 / Num. unique all: 11935 / % possible all: 72.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2O70 Resolution: 1.8→83 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.084 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.45 / ESU R: 0.147 / ESU R Free: 0.138 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.034 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→83 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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