+Open data
-Basic information
Entry | Database: PDB / ID: 7y8c | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of CotA laccase complexed with syringaldehyde | ||||||
Components | Spore coat protein A | ||||||
Keywords | OXIDOREDUCTASE / laccase | ||||||
Function / homology | Function and homology information bilirubin oxidase / laccase / sporulation resulting in formation of a cellular spore / outer membrane-bounded periplasmic space / oxidoreductase activity / copper ion binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Liu, Z.C. / Xie, T. / Wang, G.G. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2023 Title: Molecular insights into substrate promiscuity of CotA laccase catalyzing lignin-phenol derivatives. Authors: Li, J. / Liu, Z. / Zhao, J. / Wang, G. / Xie, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7y8c.cif.gz | 226 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7y8c.ent.gz | 176.9 KB | Display | PDB format |
PDBx/mmJSON format | 7y8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/7y8c ftp://data.pdbj.org/pub/pdb/validation_reports/y8/7y8c | HTTPS FTP |
---|
-Related structure data
Related structure data | 7y8bC 4q89S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 58574.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: cotA, pig, BSU06300 / Production host: Escherichia coli (E. coli) / References: UniProt: P07788 #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-PGE / | #4: Chemical | ChemComp-IJV / | #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: 2.28 Å3/Da / Density % sol: 46.06 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12-15.5% PEG 3350, 0.1M MgCl2, 0.1M pH 6.5 Bis-tris, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→48.6 Å / Num. obs: 70329 / % possible obs: 99.4 % / Redundancy: 4.4 % / CC1/2: 0.983 / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2→2.04 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 5420 / CC1/2: 0.875 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Q89 Resolution: 2→43.85 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.67 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.63 Å2 / Biso mean: 32.5442 Å2 / Biso min: 12.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→43.85 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25
|