+Open data
-Basic information
Entry | Database: PDB / ID: 2o74 | ||||||
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Title | Structure of OHCU decarboxylase in complex with guanine | ||||||
Components | OHCU decarboxylase | ||||||
Keywords | LYASE / Decarboxylation / OHCU / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline / HIU / 5-hydroxyisourate | ||||||
Function / homology | Function and homology information 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / urate catabolic process / allantoin metabolic process / purine nucleobase metabolic process / peroxisome Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Cendron, L. / Berni, R. / Folli, C. / Ramazzina, I. / Percudani, R. / Zanotti, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o74.cif.gz | 220.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o74.ent.gz | 177.1 KB | Display | PDB format |
PDBx/mmJSON format | 2o74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/2o74 ftp://data.pdbj.org/pub/pdb/validation_reports/o7/2o74 | HTTPS FTP |
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-Related structure data
Related structure data | 2o70SC 2o73C 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: ASP / Beg label comp-ID: ASP / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 2 - 164 / Label seq-ID: 2 - 164
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Details | The enzyme is a dimer in solution, there are three dimers in the asymmetric unit (AB, CD, EF) |
-Components
#1: Protein | Mass: 19768.645 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: zgc:158663 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A1L259 #2: Chemical | ChemComp-GUN / #3: 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: 2.64 Å3/Da / Density % sol: 53.43 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å |
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: 111719 / Num. obs: 111719 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 1.6 / Num. unique all: 15859 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2O70 Resolution: 1.8→88 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.97 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.142 / ESU R Free: 0.135 / 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: 24.036 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→88 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1299 / 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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