+Open data
-Basic information
Entry | Database: PDB / ID: 8kif | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of MmaE with substrate | ||||||
Components | Putative dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / MmaE / Fe/2OG enzymes | ||||||
Function / homology | : / : / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / dioxygenase activity / : / : / Putative dioxygenase Function and homology information | ||||||
Biological species | Mycobacterium marinum M (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Chen, J. / Zhou, J. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Acs Catalysis / Year: 2024 Title: Variation in biosynthesis and metal-binding properties of isonitrile-containing peptides produced by Mycobacteria versus Streptomyces. Authors: Chen, T.Y. / Chen, J. / Ruszczycky, M.W. / Hilovsky, D. / Hostetler, T. / Liu, X. / Zhou, J. / Chang, W.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8kif.cif.gz | 302.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8kif.ent.gz | 197.2 KB | Display | PDB format |
PDBx/mmJSON format | 8kif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8kif_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8kif_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8kif_validation.xml.gz | 47.7 KB | Display | |
Data in CIF | 8kif_validation.cif.gz | 67.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/8kif ftp://data.pdbj.org/pub/pdb/validation_reports/ki/8kif | HTTPS FTP |
-Related structure data
Related structure data | 8khtC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
4 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34107.648 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium marinum M (bacteria) / Gene: MMRN_02610 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Z5Y839 #2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-VY9 / ( Mass: 245.315 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H23NO4 / Feature type: SUBJECT OF INVESTIGATION #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: 2.49 Å3/Da / Density % sol: 50.67 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium acetate trihydrate, 0.1 M Tris/HCl (pH 8.5), 30% Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→61.98 Å / Num. obs: 65034 / % possible obs: 93.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 31.74 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.13→2.25 Å / Num. unique obs: 9227 / CC1/2: 0.851 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→24.48 Å / SU ML: 0.256 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.3736 / Stereochemistry target values: GeoStd + Monomer Library
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→24.48 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|