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- PDB-1y6r: Crystal structure of MTA/AdoHcy nucleosidase complexed with MT-ImmA. -
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Open data
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Basic information
Entry | Database: PDB / ID: 1y6r | ||||||
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Title | Crystal structure of MTA/AdoHcy nucleosidase complexed with MT-ImmA. | ||||||
![]() | MTA/SAH nucleosidase | ||||||
![]() | HYDROLASE / mixed alpha/beta | ||||||
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 | ![]() ![]() | ||||||
![]() | Lee, J.E. / Singh, V. / Evans, G.B. / Tyler, P.C. / Furneaux, R.H. / Cornell, K.A. / Riscoe, M.K. / Schramm, V.L. / Howell, P.L. | ||||||
![]() | ![]() Title: Structural rationale for the affinity of pico- and femtomolar transition state analogues of Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase. Authors: Lee, J.E. / Singh, V. / Evans, G.B. / Tyler, P.C. / Furneaux, R.H. / Cornell, K.A. / Riscoe, M.K. / Schramm, V.L. / Howell, P.L. #1: ![]() Title: Femtomolar transition state analogue inhibitors of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Escherichia coli. Authors: Singh, V. / Evans, G.B. / Lenz, D.H. / Painter, G.F. / Tyler, P.C. / Furneaux, R.H. / Lee, J.E. / Howell, P.L. / Schramm, V.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 | ![]() | 102.7 KB | Display | ![]() |
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PDB format | ![]() | 78.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1y6qC ![]() 1nc1S 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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Unit cell |
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Components
#1: Protein | Mass: 25488.123 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P24247, UniProt: P0AF12*PLUS, methylthioadenosine nucleosidase, adenosylhomocysteine nucleosidase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: PEG 200, sodium acetate, sodium chloride, cobaltous chloride hexahydrate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 6, 2001 / Details: mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.51418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→47.81 Å / Num. all: 27476 / Num. obs: 27476 / Observed criterion σ(F): 0 / Biso Wilson estimate: 20.4 Å2 / Limit h max: 24 / Limit h min: 0 / Limit k max: 33 / Limit k min: 0 / Limit l max: 60 / Limit l min: 0 / Observed criterion F max: 272471.28 / Observed criterion F min: 0.01 |
Reflection shell | Resolution: 2.2→2.28 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY: 1NC1 Resolution: 2.2→34.8 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 39.2875 Å2 / ksol: 0.365969 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.53 Å2 / Biso mean: 27.48 Å2 / Biso min: 7.56 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→34.8 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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