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Open data
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Basic information
Entry | Database: PDB / ID: 2mas | ||||||
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Title | PURINE NUCLEOSIDE HYDROLASE WITH A TRANSITION STATE INHIBITOR | ||||||
![]() | INOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE | ||||||
![]() | HYDROLASE / PURINE NUCLEOSIDE HYDROLASE / INOSINE / URIDINE / IU-NH / PURINE NUCLEOSIDASE | ||||||
Function / homology | ![]() inosine nucleosidase / uridine nucleosidase / inosine nucleosidase activity / uridine nucleosidase activity / nucleotide metabolic process / purine nucleoside catabolic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Degano, M. / Schramm, V.L. / Sacchettini, J.C. | ||||||
![]() | ![]() Title: Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor. Authors: Degano, M. / Almo, S.C. / Sacchettini, J.C. / Schramm, V.L. #1: ![]() Title: Three-Dimensional Structure of the Inosine-Uridine Nucleoside N-Ribohydrolase from Crithidia Fasciculata Authors: Degano, M. / Gopaul, D.N. / Scapin, G. / Schramm, V.L. / Sacchettini, J.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 | ![]() | 250.3 KB | Display | ![]() |
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PDB format | ![]() | 202.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 404.1 KB | Display | ![]() |
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Full document | ![]() | 422.8 KB | Display | |
Data in XML | ![]() | 27.2 KB | Display | |
Data in CIF | ![]() | 40.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1masS 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 34206.480 Da / Num. of mol.: 4 / Mutation: P2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-PIR / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 1.8 M AMMONIUM SULFATE, 3% ISOPROPANOL, pH 7.5 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Oct 16, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Lowest resolution: 2.3 Å / Num. obs: 73166 / % possible obs: 80.8 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.31 |
Reflection shell | Resolution: 2.3→2.5 Å / Mean I/σ(I) obs: 2.2 / % possible all: 75.1 |
Reflection | *PLUS Highest resolution: 2.3 Å |
Reflection shell | *PLUS % possible obs: 75 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: UNLIGANDED IU-NH (PDB CODE 1MAS), WATERS AND IONS REMOVED Highest resolution: 2.3 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 29.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.3 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev Biso : 1.5 Å2 / Rms dev position: 0.04 Å / Weight Biso : 3 / Weight position: 500 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.323 |