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- PDB-4pr3: Crystal structure of Brucella melitensis 5'-methylthioadenosine/S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pr3 | ||||||
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Title | Crystal structure of Brucella melitensis 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | ||||||
![]() | 5'-methylthioadenosine nucleosidase / s-adenosylhomocysteine nucleosidase | ||||||
![]() | HYDROLASE / mixed alpha/beta | ||||||
Function / homology | ![]() methylthioadenosine nucleosidase / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / nucleoside metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, X.C. / Kang, X.S. / Zhao, Y. / Jiang, D.H. / Li, X.M. / Chen, Z.L. | ||||||
![]() | ![]() Title: Crystal structure and biochemical studies of Brucella melitensis 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase Authors: Kang, X.S. / Zhao, Y. / Jiang, D.H. / Li, X.M. / Wang, X.P. / Wu, Y. / Chen, Z.L. / Zhang, X.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.8 KB | Display | ![]() |
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PDB format | ![]() | 69.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.2 KB | Display | ![]() |
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Full document | ![]() | 479.7 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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
#1: Protein | Mass: 25205.514 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8YBL1, methylthioadenosine nucleosidase, adenosylhomocysteine nucleosidase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 20%(w/v) PEG-1000, 0.1M phosphate-citrate (pH 4.2), 0.2M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 4, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 15654 / Num. obs: 15654 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 40.66 Å2 |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.38 Å2 / Biso mean: 21.55 Å2 / Biso min: 4.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.606→37.377 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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