+Open data
-Basic information
Entry | Database: PDB / ID: 1wkv | ||||||
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Title | Crystal structure of O-phosphoserine sulfhydrylase | ||||||
Components | cysteine synthase | ||||||
Keywords | TRANSFERASE / Homodimer / Open alpha/beta folding | ||||||
Function / homology | Function and homology information 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 | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Oda, Y. / Mino, K. / Ishikawa, K. / Ataka, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wkv.cif.gz | 159.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wkv.ent.gz | 131 KB | Display | PDB format |
PDBx/mmJSON format | 1wkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/1wkv ftp://data.pdbj.org/pub/pdb/validation_reports/wk/1wkv | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: APE1586 / Plasmid: pAPE1586 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) References: UniProt: Q9YBL2, Transferases; Transferring alkyl or aryl groups, other than methyl groups #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: pyridoxal 5'-phosphate, 2-mercaptoethanol, cacodylate, sodium acetate, PEG 8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9797 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 26, 2003 / Details: double crystal monochromator, bent-cylinder mirror |
Radiation | Monochromator: double crystal monochromator, bent-cylinder mirror Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 52917 / Num. obs: 52917 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.278 / Num. unique all: 4386 / Rsym value: 0.278 / % possible all: 82.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→33 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CCP4 library
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Displacement parameters | Biso mean: 27.4 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.237 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.08 Å /
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