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- PDB-6bum: Crystal structures of cyanuric acid hydrolase from Moorella therm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bum | |||||||||
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Title | Crystal structures of cyanuric acid hydrolase from Moorella thermoacetica | |||||||||
![]() | Cyanuric acid amidohydrolase![]() | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shi, K. / Cho, S. / Seffernick, J.L. / Bera, A. / Wackett, L.P. / Aihara, H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis. Authors: Shi, K. / Cho, S. / Aukema, K.G. / Lee, T. / Bera, A.K. / Seffernick, J.L. / Wackett, L.P. / Aihara, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 808 KB | Display | ![]() |
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PDB format | ![]() | 683.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6bunC ![]() 6buoC ![]() 6bupC ![]() 6buqC ![]() 6burC ![]() 6cwjC ![]() 6dhjC ![]() 3nq4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | ![]() Mass: 38484.652 Da / Num. of mol.: 4 Mutation: Q102A, E102A, K107A, L279I, K280R, F281S, E288D, L290M, A291D, K292R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 39073 / JCM 9320 / Gene: Moth_2120 / Production host: ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1200 molecules ![](data/chem/img/MLI.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MLI / ![]() #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-PDO / ![]() #5: Chemical | ChemComp-CL / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.67 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20%PEG3350, 100mMCaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.51→44.35 Å / Num. obs: 221630 / % possible obs: 95.8 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.51→1.54 Å / Redundancy: 2 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8020 / CC1/2: 0.471 / % possible all: 70.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3NQ4 Resolution: 1.51→29.993 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 13.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→29.993 Å
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Refine LS restraints |
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LS refinement shell |
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