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- PDB-5wan: Crystal Structure of a flavoenzyme RutA in the pyrimidine catabol... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wan | ||||||
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Title | Crystal Structure of a flavoenzyme RutA in the pyrimidine catabolic pathway | ||||||
![]() | Pyrimidine monooxygenase RutA | ||||||
![]() | OXIDOREDUCTASE / flavoenzyme | ||||||
Function / homology | ![]() pyrimidine oxygenase / uracil oxygenase activity / alkanesulfonate monooxygenase activity / thymine catabolic process / alkanesulfonate catabolic process / pyrimidine nucleobase catabolic process / uracil catabolic process / nitrogen utilization / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y. / Mukherjee, T. / Abdelwahed, S. / Begley, T.P. / Ealick, S.E. | ||||||
![]() | ![]() Title: Catalysis of a flavoenzyme-mediated amide hydrolysis. Authors: Mukherjee, T. / Zhang, Y. / Abdelwahed, S. / Ealick, S.E. / Begley, T.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.8 KB | Display | ![]() |
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PDB format | ![]() | 126.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 805.8 KB | Display | ![]() |
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Full document | ![]() | 808.8 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44602.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A1R1KFF4, UniProt: P75898*PLUS, pyrimidine oxygenase |
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-Non-polymers , 5 types, 276 molecules ![](data/chem/img/URA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-URA / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-FMN / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.89 % Description: THE AUTHORS STATE THAT RESIDUAL ELECTRON DENSITY WAS IDENTIFIED IN THE ACTIVE SITE DURING THE FINAL STAGES OF REFINEMENT. THE ELECTRON DENSITY COULD BE EXPLAINED AS A MIXTURE OF THE ...Description: THE AUTHORS STATE THAT RESIDUAL ELECTRON DENSITY WAS IDENTIFIED IN THE ACTIVE SITE DURING THE FINAL STAGES OF REFINEMENT. THE ELECTRON DENSITY COULD BE EXPLAINED AS A MIXTURE OF THE SUBSTRATE URACIL AND THE PRODUCT 3-UREIDOACRYLATE, EVEN THOUGH NEITHER SUBSTRATE NOR PRODUCT WAS ADDED DURING PURIFICATION OR CRYSTALLIZATION. FOR CLARITY, ONLY THE URACIL WAS INCLUDED IN THE FINAL MODEL. AS MODELED, RUTA AND URACIL DO NOT SHOW EXPECTED INTERACTIONS BASED ON THE PROPOSED MECHANISM. IN PARTICULAR, FOR THE PEROXIDE TO ADD TO THE C4 CARBONYL OF URACIL, A HYDROGEN BOND FROM AN ACID INSTEAD OF A WATER MOLECULE IS EXPECTED. ALSO NEITHER N3 NOR THE C2 CARBONYL IS INVOLVED IN HYDROGEN BONDING FROM AN ACID AS REQUIRED FOR COLLAPSE OF THE TETRAHEDRAL INTERMEDIATE. THESE INTERACTIONS COULD CONCEIVABLY BE PROVIDED BY RESIDUES 274-292, WHICH ARE DISORDERED IN THE CRYSTAL STRUCTURE. Mosaicity: 0.446 ° / Mosaicity esd: 0.004 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2 mM FMN, 1.5 M ammonium sulfate, and 100 mM MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.798→40.707 Å / Num. obs: 39453 / % possible obs: 97.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.798→1.86 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 3198 / % possible all: 80 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TVL and 1YW1 Resolution: 1.798→40.707 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.798→40.707 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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