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- PDB-6l0r: 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: 6l0r | ||||||
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Title | Crystal Structure of the O-Phosphoserine Sulfhydrylase from Aeropyrum pernix Complexed with O-Acetylserine | ||||||
![]() | Protein CysO | ||||||
![]() | TRANSFERASE / CYSTEINE BIOSYNTHESIS / SULFHYDRYLASE | ||||||
Function / homology | ![]() O-phosphoserine sulfhydrylase / O-phosphoserine sulfhydrylase activity / cystathionine beta-synthase / cysteine synthase / cystathionine beta-synthase activity / cysteine synthase activity / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Nakabayashi, M. / Takeda, E. / Ishikawa, K. / Nakamura, T. | ||||||
![]() | ![]() Title: Identification of amino acid residues important for recognition of O-phospho-l-serine substrates by cysteine synthase. Authors: Takeda, E. / Matsui, E. / Kiryu, T. / Nakagawa, T. / Nakabayashi, M. / Ishikawa, K. / Nakamura, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 294.5 KB | Display | ![]() |
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PDB format | ![]() | 238.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 52 KB | Display | |
Data in CIF | ![]() | 71.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6l0pC ![]() 6l0qC ![]() 6l0sC ![]() 5b3aS S: Starting model for refinement C: citing same article ( |
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Similar 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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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41897.637 Da / Num. of mol.: 4 / Mutation: K127A, F225Y, R297A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9YBL2, cystathionine beta-synthase, cysteine synthase, O-phosphoserine sulfhydrylase #2: Chemical | ChemComp-E1R / ( #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.07 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium N-2-hydroxyethylpiperazine-N'-2-ethanesulfonate buffer, pH 8.2 (7.9), 29% (v/v) 2-propanol, 13% (11%) (v/v) polyethylene glycol 4,000, and 11 mM TCEP-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jul 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→74.46 Å / Num. obs: 139467 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.79→1.89 Å / Rmerge(I) obs: 0.835 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 20355 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5B3A Resolution: 1.79→74.46 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1701 / WRfactor Rwork: 0.163 / FOM work R set: 0.951 / SU B: 1.127 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0988 / SU Rfree: 0.0816 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.46 Å2 / Biso mean: 24.612 Å2 / Biso min: 6.22 Å2
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Refinement step | Cycle: final / Resolution: 1.79→74.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.794→1.841 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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