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- PDB-3o4v: Crystal structure of E. coli MTA/SAH nucleosidase in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3o4v | ||||||
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Title | Crystal structure of E. coli MTA/SAH nucleosidase in complex with (4-Chlorophenyl)thio-DADMe-ImmA | ||||||
![]() | MTA/SAH nucleosidase | ||||||
![]() | HYDROLASE / mixed alpha/beta dimer | ||||||
Function / homology | ![]() toxic metabolite repair / purine deoxyribonucleoside catabolic process / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Siu, K.K.W. / Howell, P.L. | ||||||
![]() | ![]() Title: Crystal structure of E. coli MTA/SAH nucleosidase in complex with (4-Chlorophenyl)thio-DADMe-ImmA Authors: Siu, K.K.W. / Howell, P.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.2 KB | Display | ![]() |
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PDB format | ![]() | 85.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1014.6 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 24612.174 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: D3QWG1, UniProt: P0AF12*PLUS, adenosylhomocysteine nucleosidase, methylthioadenosine nucleosidase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-IPA / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 4.6 Details: 60 mM Sodium acetate, pH 4.6, 35% (v/v) isopropanol, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 20, 2005 / Details: MIRRORS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: CONFOCAL MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→32.93 Å / Num. obs: 46533 / % possible obs: 98.8 % / Redundancy: 12.31 % / Rmerge(I) obs: 0.049 / Χ2: 0.93 / Net I/σ(I): 29.5 / Scaling rejects: 30157 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.83 Å2 / Biso mean: 14.5508 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→21.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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