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- PDB-3vsc: Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vsc | ||||||
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Title | Crystal Structure of the K127A Mutant of O-Phosphoserine Sulfhydrylase Complexed with External Schiff Base of Pyridoxal 5'-Phosphate with O-Phospho-L-Serine | ||||||
![]() | Protein CysO | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakamura, T. / Kawai, Y. / Kataoka, M. / Ishikawa, K. | ||||||
![]() | ![]() Title: Structural analysis of the substrate recognition mechanism in O-phosphoserine sulfhydrylase from the hyperthermophilic archaeon Aeropyrum pernix K1 Authors: Nakamura, T. / Kawai, Y. / Kunimoto, K. / Iwasaki, Y. / Nishii, K. / Kataoka, M. / Ishikawa, K. #1: ![]() Title: Three-dimensional structure of a new enzyme, O-phosphoserine sulfhydrylase, involved in l-cysteine biosynthesis by a hyperthermophilic archaeon, Aeropyrum pernix K1, at 2.0A resolution Authors: Oda, Y. / Mino, K. / Ishikawa, K. / Ataka, M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 158 KB | Display | ![]() |
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PDB format | ![]() | 130.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Components
#1: Protein | Mass: 41967.754 Da / Num. of mol.: 2 / Mutation: K127A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9YBL2, ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-MPD / ( | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.36 % / Mosaicity: 0.798 ° |
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Crystal grow![]() | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES sodium pH 7.5, 25% 2-propanol, 10% PEG 4000, 5mM O-phospho-L-serine, 5mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2009 / Details: rhodium-coated mirrors (horizontal and vertical) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rotated-inclined double-crystal monochromator , Si (111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.07→50 Å / Num. obs: 48366 / % possible obs: 99.2 % / Redundancy: 8 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.079 / Χ2: 1.202 / Net I/σ(I): 9.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 81.72 Å2 / Biso mean: 35.3454 Å2 / Biso min: 16.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.073→2.127 Å / Total num. of bins used: 20
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