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- PDB-1nc3: Crystal structure of E. coli MTA/AdoHcy nucleosidase complexed wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nc3 | ||||||
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Title | Crystal structure of E. coli MTA/AdoHcy nucleosidase complexed with formycin A (FMA) | ||||||
![]() | 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 | ![]() ![]() | ||||||
![]() | Lee, J.E. / Cornell, K.A. / Riscoe, M.K. / Howell, P.L. | ||||||
![]() | ![]() Title: Structure of Escherichia coli 5'-methylthioadenosine/ S-adenosylhomocysteine nucleosidase inhibitor complexes provide insight into the conformational changes required for substrate binding and catalysis. Authors: Lee, J.E. / Cornell, K.A. / Riscoe, M.K. / 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 | ![]() | 101.1 KB | Display | ![]() |
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PDB format | ![]() | 77.6 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 | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nc1C ![]() 1jysS 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, adenosylhomocysteine nucleosidase #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | Waters 1-98 are associated with chain A and waters 99-200 are associated with chain B. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.88 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: PEG 200, sodium acetate, sodium chloride, cobalt chloride, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 12, 2001 / Details: Confocal multilayer |
Radiation | Monochromator: Confocal multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→47.48 Å / Num. obs: 23876 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.072 |
Reflection shell | Resolution: 2.2→2.34 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.22 / Num. unique all: 3920 / % possible all: 99.8 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. obs: 29777 / % possible obs: 99.8 % / Redundancy: 5.7 % / Num. measured all: 170060 / Rmerge(I) obs: 0.077 |
Reflection shell | *PLUS Lowest resolution: 2.3 Å / % possible obs: 99.5 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB code: 1JYS Resolution: 2.2→47.48 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 29.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→47.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.022
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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