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- PDB-2yzb: Crystal structure of uricase from Arthrobacter globiformis in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yzb | ||||||
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Title | Crystal structure of uricase from Arthrobacter globiformis in complex with uric acid (substrate) | ||||||
![]() | Uricase | ||||||
![]() | OXIDOREDUCTASE / uricase / uric acid | ||||||
Function / homology | ![]() purine nucleobase catabolic process / urate oxidase activity / factor-independent urate hydroxylase / urate catabolic process / peroxisome Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Juan, E.C.M. / Hossain, M.T. / Hoque, M.M. / Suzuki, K. / Sekiguchi, T. / Takenaka, A. | ||||||
![]() | ![]() Title: Trapping of the uric acid substrate in the crystal structure of urate oxidase from Arthrobacter globiformis Authors: Juan, E.C.M. / Hossain, M.T. / Hoque, M.M. / Yamamoto, T. / Imamura, S. / Suzuki, K. / Sekiguchi, T. / Takenaka, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 475.7 KB | Display | ![]() |
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PDB format | ![]() | 391.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2yzcC ![]() 2yzdC ![]() 2yzeC ![]() 1uox C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33900.629 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: D0VWQ1*PLUS, factor-independent urate hydroxylase #2: Chemical | ChemComp-URC / #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE DATABASE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNP. IT WILL BE SUBMITTED TO UNP ...THE SEQUENCE DATABASE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNP. IT WILL BE SUBMITTED TO UNP DATABASE SOON. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG 8000, lithium sulfate, sodium borate buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 3, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 213158 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.09 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.341 / % possible all: 73.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1uox ![]() 1uox Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 3
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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