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Yorodumi- PDB-8oiw: Crystal structure of the cysteine-rich Gallus gallus urate oxidas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oiw | |||||||||
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Title | Crystal structure of the cysteine-rich Gallus gallus urate oxidase in complex with the 8-azaxanthine inhibitor under oxidising conditions (space group P 21 21 21) | |||||||||
Components | (Uricase) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / COFACTOR-FREE OXIDASE / INHIBITOR / DIOXYGEN BINDING / CYSTEINE | |||||||||
Function / homology | factor-independent urate hydroxylase / Uricase / Uricase / purine nucleobase metabolic process / peroxisome / oxidoreductase activity / 8-AZAXANTHINE / OXYGEN MOLECULE / Uricase Function and homology information | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | |||||||||
Authors | Di Palma, M. / Chegkazi, M. / Bui, S. / Mori, G. / Percudani, R. / Steiner, R.A. | |||||||||
Funding support | United Kingdom, Italy, 2items
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Citation | Journal: Mol.Biol.Evol. / Year: 2023 Title: Cysteine Enrichment Mediates Co-Option of Uricase in Reptilian Skin and Transition to Uricotelism. Authors: Mori, G. / Liuzzi, A. / Ronda, L. / Di Palma, M. / Chegkazi, M.S. / Bui, S. / Garcia-Maya, M. / Ragazzini, J. / Malatesta, M. / Della Monica, E. / Rivetti, C. / Antin, P.B. / Bettati, S. / ...Authors: Mori, G. / Liuzzi, A. / Ronda, L. / Di Palma, M. / Chegkazi, M.S. / Bui, S. / Garcia-Maya, M. / Ragazzini, J. / Malatesta, M. / Della Monica, E. / Rivetti, C. / Antin, P.B. / Bettati, S. / Steiner, R.A. / Percudani, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oiw.cif.gz | 486.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oiw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8oiw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oiw_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 8oiw_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 8oiw_validation.xml.gz | 50.6 KB | Display | |
Data in CIF | 8oiw_validation.cif.gz | 70.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/8oiw ftp://data.pdbj.org/pub/pdb/validation_reports/oi/8oiw | HTTPS FTP |
-Related structure data
Related structure data | 8ofkC 8oh8C 8oihC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein , 2 types, 4 molecules AAABBBCCCDDD
#1: Protein | Mass: 39189.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LOC101747367 / Production host: Escherichia coli (E. coli) References: UniProt: A0A8V0ZED1, factor-independent urate hydroxylase |
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#2: Protein | Mass: 39205.883 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LOC101747367 / Production host: Escherichia coli (E. coli) References: UniProt: A0A8V0ZED1, factor-independent urate hydroxylase |
-Non-polymers , 5 types, 629 molecules
#3: Chemical | ChemComp-AZA / #4: Chemical | ChemComp-OXY / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.67 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: His6-tagged GgUOX at approx. 22 mg/ml in 50 mM Tris-HCl pH 8.0, 10 mM NaCl, 1 mM TCEP-HCl was incubated with a 20-fold molar excess of AZA. Crystals were obtained by mixing the protein with ...Details: His6-tagged GgUOX at approx. 22 mg/ml in 50 mM Tris-HCl pH 8.0, 10 mM NaCl, 1 mM TCEP-HCl was incubated with a 20-fold molar excess of AZA. Crystals were obtained by mixing the protein with 0.8M K/Na tartrate tetrahydrate, 0.1 M HEPES pH 7.5 using a 1:1 ratio. Crystals were transferred into cryoprotective solutions supplemented with 100 mM H2O2 and devoid of the TCEP-HCl reducing agent for approximately 15 minutes prior to cryocooling in liquid nitrogen. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97948 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→78.89 Å / Num. obs: 131041 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.048 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.89→1.92 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 6365 / CC1/2: 0.253 / Rpim(I) all: 0.123 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→78.888 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 10.963 / SU ML: 0.141 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.122 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.869 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→78.888 Å
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Refine LS restraints |
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