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Yorodumi- PDB-9prr: X-ray crystal structure of Streptomyces cacaoi PolF in complex wi... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9prr | ||||||
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| Title | X-ray crystal structure of Streptomyces cacaoi PolF in complex with iron and L-isoleucine | ||||||
Components | PolF | ||||||
Keywords | OXIDOREDUCTASE / polyoximic acid / diiron cofactor / biosynthesis / cyclization / heme-oxygenase-like diiron enzyme / BIOSYNTHETIC PROTEIN | ||||||
| Function / homology | : / ISOLEUCINE Function and homology information | ||||||
| Biological species | Streptomyces cacaoi (bacteria) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Blancas Cortez, J.J. / Boal, A.K. | ||||||
| Funding support | United States, 1items
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Citation | Journal: Nat.Chem. / Year: 2025Title: Azetidine amino acid biosynthesis by non-haem iron-dependent enzymes. Authors: Du, Y. / Thanapipatsiri, A. / Blancas Cortez, J.J. / Salas-Sola, X.E. / Lin, C.Y. / Boal, A.K. / Krebs, C. / Bollinger Jr., J.M. / Yokoyama, K. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9prr.cif.gz | 741.1 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9prr.ent.gz | 511 KB | Display | PDB format |
| PDBx/mmJSON format | 9prr.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9prr_validation.pdf.gz | 6.9 MB | Display | wwPDB validaton report |
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| Full document | 9prr_full_validation.pdf.gz | 6.9 MB | Display | |
| Data in XML | 9prr_validation.xml.gz | 64.2 KB | Display | |
| Data in CIF | 9prr_validation.cif.gz | 82 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/9prr ftp://data.pdbj.org/pub/pdb/validation_reports/pr/9prr | HTTPS FTP |
-Related structure data
| Related structure data | |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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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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| 3 | ![]()
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| Unit cell |
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Components
-Protein , 1 types, 6 molecules ABCDEF
| #1: Protein | Mass: 30167.922 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: The originally expressed polypeptide construct possessed the extra sequence MGSSHHHHHHSSGLVPRGSHGENLYFQ at the N-terminus. This sequence included a His6, thrombin recognition, TEV- ...Details: The originally expressed polypeptide construct possessed the extra sequence MGSSHHHHHHSSGLVPRGSHGENLYFQ at the N-terminus. This sequence included a His6, thrombin recognition, TEV-recognition sequence, and linkers between them. This extra sequence was cleaved off the construct through TEV incubation and removed from protein solution through Ni-NTA and S200 purification. Source: (gene. exp.) Streptomyces cacaoi (bacteria) / Production host: ![]() |
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-Non-polymers , 5 types, 169 molecules 








| #2: Chemical | | #3: Chemical | ChemComp-FE2 / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-ILE / #6: Water | ChemComp-HOH / | |
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-Details
| Has ligand of interest | Y |
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| Has protein modification | N |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.53 % |
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| Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.5 M Lithium Chloride, 0.1 M Tris PH 7.6, 15% (w/v) PEG 6000 |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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| Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.919689 Å |
| Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 13, 2025 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.919689 Å / Relative weight: 1 |
| Reflection | Resolution: 2.06→34.16 Å / Num. obs: 51376 / % possible obs: 91.69 % / Redundancy: 6.81 % / Biso Wilson estimate: 27.27 Å2 / CC1/2: 0.973 / Net I/σ(I): 7.6 |
| Reflection shell | Resolution: 2.06→2.7 Å / Num. unique obs: 5703 / CC1/2: 0.67 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→34.16 Å / SU ML: 0.1964 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8316 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 30.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.06→34.16 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: 37.905 Å / Origin y: 17.042 Å / Origin z: -23.093 Å
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| Refinement TLS group |
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About Yorodumi



Streptomyces cacaoi (bacteria)
X-RAY DIFFRACTION
United States, 1items
Citation
PDBj







