[English] 日本語
Yorodumi- PDB-5daq: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5daq | ||||||
---|---|---|---|---|---|---|---|
Title | Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ in complex with 4-Methoxycyclopeptin | ||||||
Components | Phytanoyl-CoA dioxygenase family protein (AFU_orthologue AFUA_8G00230) | ||||||
Keywords | OXIDOREDUCTASE / Antibiotics / Biosynthesis / Alkaloids / Viridicatin / Desaturase / Epoxidase / Fragmentation / 4-Methoxycyclopeptine | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Emericella nidulans (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Groll, M. / Braeuer, A. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2016 Title: Structure of the Dioxygenase AsqJ: Mechanistic Insights into a One-Pot Multistep Quinolone Antibiotic Biosynthesis. Authors: Brauer, A. / Beck, P. / Hintermann, L. / Groll, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5daq.cif.gz | 141.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5daq.ent.gz | 109.2 KB | Display | PDB format |
PDBx/mmJSON format | 5daq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/5daq ftp://data.pdbj.org/pub/pdb/validation_reports/da/5daq | HTTPS FTP |
---|
-Related structure data
Related structure data | 5dapSC 5davC 5dawC 5daxC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 33978.855 Da / Num. of mol.: 1 / Fragment: UNP residues 110-416 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold) Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: AN9227.2, ANIA_09227 / Plasmid: pET28b(+) / Details (production host): Cleavable SUMO-fusion tag / Production host: Escherichia coli (E. coli) / References: UniProt: Q5AR53 |
---|---|
#2: Chemical | ChemComp-NI / |
#3: Chemical | ChemComp-AKG / |
#4: Chemical | ChemComp-58D / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 43 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM TRIS/HCl, 1 M LiBr, 27% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2015 |
Radiation | Monochromator: LN2 COOLED FIXED-EXIT. SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 32625 / Num. obs: 32005 / % possible obs: 98.1 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.7→1.8 Å / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2.8 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DAP Resolution: 1.7→15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 6.045 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 29.326 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.7→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|