+Open data
-Basic information
Entry | Database: PDB / ID: 8jz3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of AetF in complex with FAD and L-tryptophan | ||||||
Components | AetF | ||||||
Keywords | FLAVOPROTEIN / halogenase / flavin-dependent / single-component / L-tryptophan | ||||||
Function / homology | FAD/NAD(P)-binding domain superfamily / nucleotide binding / metal ion binding / FLAVIN-ADENINE DINUCLEOTIDE / TRYPTOPHAN / AetF Function and homology information | ||||||
Biological species | Aetokthonos hydrillicola Thurmond2011 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Li, H. / Dai, L. / Chen, C.-C. / Guo, R.-T. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2024 Title: Structural and functional insights into the self-sufficient flavin-dependent halogenase. Authors: Dai, L. / Li, H. / Dai, S. / Zhang, Q. / Zheng, H. / Hu, Y. / Guo, R.T. / Chen, C.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8jz3.cif.gz | 155.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8jz3.ent.gz | 116.7 KB | Display | PDB format |
PDBx/mmJSON format | 8jz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jz3_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8jz3_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8jz3_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 8jz3_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/8jz3 ftp://data.pdbj.org/pub/pdb/validation_reports/jz/8jz3 | HTTPS FTP |
-Related structure data
Related structure data | 8jz2C 8jz4C 8jz5C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 78556.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aetokthonos hydrillicola Thurmond2011 (bacteria) Gene: aetF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A861B9Z9 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-FAD / | ||||
#3: Chemical | #4: 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: 1.98 Å3/Da / Density % sol: 38.03 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 30% PEG 6000, 0.1 M Tris pH 8.0, 8 mg/mL AetF (5 mM L-Trp, 5 mM DTT) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Jun 15, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34138 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→33.16 Å / Num. obs: 32585 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.997 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.2→2.23 Å / Num. unique obs: 1260 / CC1/2: 0.803 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→33.16 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.908 / SU B: 9.922 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.272 / 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: 38.467 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.2→33.16 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|