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Yorodumi- PDB-8i28: Structure of Phosphoserine Aminotransferase from Saccharomyces ce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i28 | ||||||
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Title | Structure of Phosphoserine Aminotransferase from Saccharomyces cerevisiae | ||||||
Components | Phosphoserine aminotransferase | ||||||
Keywords | TRANSFERASE / Phosphoserine | ||||||
Function / homology | Function and homology information Serine biosynthesis / serine family amino acid biosynthetic process / phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / purine nucleobase biosynthetic process / L-serine biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Jang, J.Y. / Chang, J.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Molecular Structure of Phosphoserine Aminotransferase from Saccharomyces cerevisiae. Authors: Jang, J. / Chang, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i28.cif.gz | 270.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i28.ent.gz | 220 KB | Display | PDB format |
PDBx/mmJSON format | 8i28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i28_validation.pdf.gz | 443 KB | Display | wwPDB validaton report |
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Full document | 8i28_full_validation.pdf.gz | 457.2 KB | Display | |
Data in XML | 8i28_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 8i28_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/8i28 ftp://data.pdbj.org/pub/pdb/validation_reports/i2/8i28 | HTTPS FTP |
-Related structure data
Related structure data | 6czxS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43470.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SER1, SERC, YOR184W / Production host: Escherichia coli (E. coli) / References: UniProt: P33330, phosphoserine transaminase #2: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 4.08 Å3/Da / Density % sol: 69.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2.4 M ammonium sulfate and 0.1 M citric acid (pH 3.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 35761 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 18.75 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 3519 / CC1/2: 0.506 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CZX Resolution: 2.8→48.33 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→48.33 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 74.7884 Å / Origin y: 34.3092 Å / Origin z: 71.4581 Å
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Refinement TLS group | Selection details: all |