+Open data
-Basic information
Entry | Database: PDB / ID: 8a82 | ||||||
---|---|---|---|---|---|---|---|
Title | Fe(II)/aKG-dependent halogenase OocPQ | ||||||
Components |
| ||||||
Keywords | BIOSYNTHETIC PROTEIN / Halogenase / Polyketide Synthase / Biosynthesis / Metal Catalysis | ||||||
Function / homology | Cupin-like domain 8 / Cupin-like domain / : / Cupin-like domain-containing protein / Uncharacterized protein Function and homology information | ||||||
Biological species | Serratia plymuthica 4Rx13 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å | ||||||
Authors | Fraley, A.E. / Meoded, R.A. / Schmalhofer, M. / Bergande, C. / Groll, M. / Piel, J. | ||||||
Funding support | Switzerland, 1items
| ||||||
Citation | Journal: Structure / Year: 2023 Title: Heterocomplex structure of a polyketide synthase component involved in modular backbone halogenation. Authors: Fraley, A.E. / Dell, M. / Schmalhofer, M. / Meoded, R.A. / Bergande, C. / Groll, M. / Piel, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8a82.cif.gz | 211.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8a82.ent.gz | 168.4 KB | Display | PDB format |
PDBx/mmJSON format | 8a82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a82_validation.pdf.gz | 1003.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8a82_full_validation.pdf.gz | 1007 KB | Display | |
Data in XML | 8a82_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 8a82_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/8a82 ftp://data.pdbj.org/pub/pdb/validation_reports/a8/8a82 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 45233.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia plymuthica 4Rx13 (bacteria) / Gene: oocP / Production host: Escherichia coli (E. coli) / References: UniProt: K7WEY7 |
---|---|
#2: Protein | Mass: 14031.038 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia plymuthica 4Rx13 (bacteria) / Gene: oocQ, ALQ63_00827, CT690_01890 / Production host: Escherichia coli (E. coli) / References: UniProt: K7XCU4 |
#3: Chemical | ChemComp-FE / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.96 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Bicine, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 38390 / % possible obs: 97.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.05→2.15 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5062 / % possible all: 96.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 10.788 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.284 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 124.21 Å2 / Biso mean: 50.502 Å2 / Biso min: 32.41 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|