[English] 日本語

- PDB-9prr: X-ray crystal structure of Streptomyces cacaoi PolF in complex wi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 9prr | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray crystal structure of Streptomyces cacaoi PolF in complex with iron and L-isoleucine | ||||||
![]() | PolF | ||||||
![]() | OXIDOREDUCTASE / polyoximic acid / diiron cofactor / biosynthesis / cyclization / heme-oxygenase-like diiron enzyme / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | : / ISOLEUCINE![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Blancas Cortez, J.J. / Boal, A.K. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Azetidine amino acid biosynthesis by non-heme iron-dependent enzymes Authors: Du, Y. / Thanapipatsiri, A. / Salas Sola, X.E. / Blancas Cortez, J.J. / Lin, C.Y. / Boal, A.K. / Krebs, C. / Bollinger, J.M. / Yokoyama, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 740.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 510.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 6.9 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 6.9 MB | Display | |
Data in XML | ![]() | 64.2 KB | Display | |
Data in CIF | ![]() | 82 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9mri |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
3 | ![]()
| ||||||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 169 molecules 








#2: Chemical | #3: Chemical | ChemComp-FE2 / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-ILE / #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|---|
Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.53 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 37.905 Å / Origin y: 17.042 Å / Origin z: -23.093 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|