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- PDB-5b36: Crystal Structure of the O-Phosphoserine Sulfhydrylase from Aerop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b36 | ||||||
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Title | Crystal Structure of the O-Phosphoserine Sulfhydrylase from Aeropyrum pernix Complexed with Cysteine | ||||||
![]() | Protein CysO | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakamura, T. / Takeda, E. / Kawai, Y. / Kataoka, M. / Ishikawa, K. | ||||||
![]() | ![]() Title: Role of F225 in O-phosphoserine sulfhydrylase from Aeropyrum pernix K1 Authors: Takeda, E. / Kunimoto, K. / Kawai, Y. / Kataoka, M. / Ishikawa, K. / Nakamura, T. #1: ![]() 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. #2: ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.7 KB | Display | ![]() |
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PDB format | ![]() | 130.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5b3aC ![]() 3vsaS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42025.855 Da / Num. of mol.: 2 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: 46.24 % |
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Crystal grow![]() | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES sodium pH 7.5, 27% 2-propanol, 10% PEG4000, 12 mM TCEP-HCl, the crystal was soaked with the reservoir solution containing 6% MPD as a cryoprotectant, 20 mM L-cysteine, and 12 mM TCEP-HCl |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jan 29, 2010 |
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: 2.15→49.1 Å / Num. obs: 43621 / % possible obs: 92 % / Redundancy: 13.5 % / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.14→2.18 Å |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: CysO free form (PDB ID, 3VSA) Resolution: 2.15→49.1 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.615 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.224 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.235 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→49.1 Å
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Refine LS restraints |
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