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- PDB-1w2w: Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1w2w | ||||||
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Title | Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits | ||||||
![]() | (5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE) x 2 | ||||||
![]() | ISOMERASE / EIF2B / METHIONINE SALVAGE PATHWAY / TRANSLATION INITIATION / OXIDOREDUCTASE | ||||||
Function / homology | ![]() Methionine salvage pathway / S-methyl-5-thioribose-1-phosphate isomerase / S-methyl-5-thioribose-1-phosphate isomerase activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bumann, M. / Djafarzadeh, S. / Oberholzer, A.E. / Bigler, P. / Altmann, M. / Trachsel, H. / Baumann, U. | ||||||
![]() | ![]() Title: Crystal Structure of Yeast Ypr118W, a Methylthioribose-1-Phosphate Isomerase Related to Regulatory Eif2B Subunits Authors: Bumann, M. / Djafarzadeh, S. / Oberholzer, A.E. / Bigler, P. / Altmann, M. / Trachsel, H. / Baumann, U. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BD, FD" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BD, FD" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 4-STRANDED BARRELS WHICH ARE REPRESENTED BY 5-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 323.4 KB | Display | ![]() |
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PDB format | ![]() | 274.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 406.3 KB | Display | ![]() |
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Full document | ![]() | 417.7 KB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 51.7 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 23353.072 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-211 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PGEX-6P3 / Production host: ![]() ![]() References: UniProt: Q06489, S-methyl-5-thioribose-1-phosphate isomerase #2: Protein | Mass: 21031.689 Da / Num. of mol.: 4 / Fragment: RESIDUES 221-411 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PGEX-6P3 / Production host: ![]() ![]() References: UniProt: Q06489, S-methyl-5-thioribose-1-phosphate isomerase #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.5 % |
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Crystal grow | Temperature: 293 K Details: 0.2 M AMMONIUM SULPHATE, 25 % PEG3350, 0.1 M BISTRIS, PH 5.5, 20 DEG C |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9879 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. obs: 169966 / % possible obs: 99.6 % / Observed criterion σ(I): 4.1 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.75→1.87 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→30 Å
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Refine LS restraints |
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