+Open data
-Basic information
Entry | Database: PDB / ID: 8gyh | |||||||||||||||
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Title | Crystal structure of Fic25 (apo form) from Streptomyces ficellus | |||||||||||||||
Components | DegT/DnrJ/EryC1/StrS family aminotransferase | |||||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / Sugar aminotransferase / Biosynthetic enzyme / DADH | |||||||||||||||
Function / homology | Function and homology information dTDP-4-amino-4,6-dideoxygalactose transaminase activity / polysaccharide biosynthetic process / antibiotic biosynthetic process / pyridoxal phosphate binding Similarity search - Function | |||||||||||||||
Biological species | Streptomyces ficellus (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||||||||
Authors | Kurosawa, S. / Yoshida, A. / Tomita, T. / Nishiyama, M. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: Acs Chem.Biol. / Year: 2023 Title: Mechanisms of Sugar Aminotransferase-like Enzymes to Synthesize Stereoisomers of Non-proteinogenic Amino Acids in Natural Product Biosynthesis. Authors: Kurosawa, S. / Okamura, H. / Yoshida, A. / Tomita, T. / Sone, Y. / Hasebe, F. / Shinada, T. / Takikawa, H. / Kosono, S. / Nishiyama, M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gyh.cif.gz | 188.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gyh.ent.gz | 147.4 KB | Display | PDB format |
PDBx/mmJSON format | 8gyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gyh_validation.pdf.gz | 469 KB | Display | wwPDB validaton report |
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Full document | 8gyh_full_validation.pdf.gz | 473.8 KB | Display | |
Data in XML | 8gyh_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 8gyh_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/8gyh ftp://data.pdbj.org/pub/pdb/validation_reports/gy/8gyh | HTTPS FTP |
-Related structure data
Related structure data | 8gyiC 8gyjC C: citing same article (ref.) |
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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: 46911.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces ficellus (bacteria) / Gene: EIZ62_06105 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W5T2G9 #2: Chemical | ChemComp-GOL / | #3: Chemical | ChemComp-IMD / #4: 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: 3.57 Å3/Da / Density % sol: 65.5 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 1.0 M Sodium citrate, 0.1 M Imidazole, pH8.0 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.484 Å / Num. obs: 122992 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.94 / Num. unique obs: 6059 / CC1/2: 0.835 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model constructed by AlphaFold2 from the primary amino acid sequence of Fic25 Resolution: 1.8→48.48 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.223 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.087 / 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: 83.56 Å2 / Biso mean: 21.536 Å2 / Biso min: 11.7 Å2
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Refinement step | Cycle: final / Resolution: 1.8→48.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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