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- PDB-2h6u: Crystal structure of 5-hydroxyisourate hydrolase (formerly known ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2h6u | ||||||
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Title | Crystal structure of 5-hydroxyisourate hydrolase (formerly known as TRP, transthyretin related protein) | ||||||
![]() | 5-HYDROXYISOURATE HYDROLASE (FORMERLY KNOWN AS TRP, TRANSTHYRETIN RELATED PROTEIN) | ||||||
![]() | HYDROLASE / 5-HYDROXYISOURATE HYDROLASE / TRP / URIC ACID DEGRADATION / ALLANTOIN | ||||||
Function / homology | ![]() hydroxyisourate hydrolase / hydroxyisourate hydrolase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / urate catabolic process / purine nucleobase metabolic process / peroxisome Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zanotti, G. / Cendron, L. / Folli, C. / Ramazzina, I. / Percudani, R. / Berni, R. | ||||||
![]() | ![]() Title: Structure of Zebra fish HIUase: Insights into Evolution of an Enzyme to a Hormone Transporter. Authors: Zanotti, G. / Cendron, L. / Ramazzina, I. / Folli, C. / Percudani, R. / Berni, R. #1: ![]() Title: Completing the Uric Acid Degradation Pathway Through Phylogenetic Comparison of Whole Genomes Authors: Ramazzina, I. / Folli, C. / Secchi, A. / Berni, R. / 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 | ![]() | 198.9 KB | Display | ![]() |
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PDB format | ![]() | 159.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.8 KB | Display | ![]() |
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Full document | ![]() | 488.4 KB | Display | |
Data in XML | ![]() | 40.1 KB | Display | |
Data in CIF | ![]() | 57.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2h1xSC 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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2 | ![]()
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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: LEU / Beg label comp-ID: LEU / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 6 / Auth seq-ID: 6 - 119 / Label seq-ID: 6 - 119
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Details | The biological unit is a homo-tetramer. Two of such tetramers are present in the asymmetric unit. |
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Components
#1: Protein | Mass: 13260.125 Da / Num. of mol.: 8 / Mutation: S2A, P6L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q0P422, UniProt: Q06S87*PLUS, hydroxyisourate hydrolase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% (w/v) PEG 10000, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→118 Å / Num. all: 103601 / Num. obs: 103601 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 3 / Num. unique all: 12933 / % possible all: 80.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 2H1X Resolution: 1.7→64.2 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.553 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.136 / ESU R Free: 0.128 / 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: 18.467 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→64.2 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 901 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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