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Yorodumi- PDB-2h1x: Crystal structure of 5-hydroxyisourate Hydrolase (formerly known ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h1x | ||||||
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Title | Crystal structure of 5-hydroxyisourate Hydrolase (formerly known as TRP, Transthyretin Related Protein) | ||||||
Components | 5-hydroxyisourate Hydrolase (formerly known as TRP, Transthyretin Related Protein) | ||||||
Keywords | HYDROLASE / 5-hydroxyisourate Hydrolase / TRP / uric acid degradation / allantoin | ||||||
Function / homology | Function and homology information 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 | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Zanotti, G. / Cendron, L. / Folli, C. / Ramazzina, I. / Percudani, R. / Berni, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 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: Journal: NAT.CHEM.BIOL. / Year: 2006 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h1x.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h1x.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 2h1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h1x_validation.pdf.gz | 451.8 KB | Display | wwPDB validaton report |
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Full document | 2h1x_full_validation.pdf.gz | 462.8 KB | Display | |
Data in XML | 2h1x_validation.xml.gz | 20 KB | Display | |
Data in CIF | 2h1x_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/2h1x ftp://data.pdbj.org/pub/pdb/validation_reports/h1/2h1x | HTTPS FTP |
-Related structure data
Related structure data | 2h6uC 1f41S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 7 - 119 / Label seq-ID: 7 - 119
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Details | The homo-tetramer present in the asymmetric unit coincides with the biological assembly |
-Components
#1: Protein | Mass: 13260.125 Da / Num. of mol.: 4 / Mutation: S2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: GeneID:558664 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: Q0P422, UniProt: Q06S87*PLUS, hydroxyisourate hydrolase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, 20% PEG 10000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2006 / Details: Toroidal mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→500 Å / Num. all: 26947 / Num. obs: 26947 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3574 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F41 Resolution: 1.98→58.82 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.35 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.19 / ESU R: 0.252 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 25.05 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.98→58.82 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: 1.98→2.031 Å / Total num. of bins used: 20
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