+Open data
-Basic information
Entry | Database: PDB / ID: 7etl | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of FtmOx1-Y68F | ||||||
Components | Verruculogen synthase | ||||||
Keywords | OXIDOREDUCTASE / non-heme iron enzyme / endoperoxide / mutant | ||||||
Function / homology | Function and homology information verruculogen synthase / verruculogen biosynthetic process / dioxygenase activity Similarity search - Function | ||||||
Biological species | Aspergillus fumigatus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99212801333 Å | ||||||
Authors | Zhou, J.H. / Wu, L. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022 Title: Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1. Authors: Wu, L. / Wang, Z. / Cen, Y. / Wang, B. / Zhou, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7etl.cif.gz | 163.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7etl.ent.gz | 102.9 KB | Display | PDB format |
PDBx/mmJSON format | 7etl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7etl_validation.pdf.gz | 761.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7etl_full_validation.pdf.gz | 763.8 KB | Display | |
Data in XML | 7etl_validation.xml.gz | 24 KB | Display | |
Data in CIF | 7etl_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/7etl ftp://data.pdbj.org/pub/pdb/validation_reports/et/7etl | HTTPS FTP |
-Related structure data
Related structure data | 7etkC 4zon S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35066.023 Da / Num. of mol.: 2 / Mutation: Y68F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: ftmOx1 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q4WAW9, verruculogen synthase |
---|
-Non-polymers , 7 types, 241 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-AKG / | #6: Chemical | ChemComp-FE2 / | #7: Chemical | ChemComp-EDO / | #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.91 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-tris pH 7.0, 1.9 M ammonium sulfate,0,05 M CoCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 38521 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 25.6288877739 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.175 / Rsym value: 0.175 / Net I/σ(I): 10.125 |
Reflection shell | Resolution: 1.99→2.02 Å / Rmerge(I) obs: 0.877 / Num. unique obs: 1881 / CC1/2: 0.539 / Rsym value: 0.877 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZON 4zon Resolution: 1.99212801333→27.7054821166 Å / SU ML: 0.233602024323 / Cross valid method: FREE R-VALUE / σ(F): 1.35031747064 / Phase error: 21.5983391972 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.6674714723 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99212801333→27.7054821166 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|