+Open data
-Basic information
Entry | Database: PDB / ID: 8bib | ||||||
---|---|---|---|---|---|---|---|
Title | O-Methyltransferase Plu4890 in complex with SAH and AQ-256 | ||||||
Components | Methyltransferase Plu4890 | ||||||
Keywords | TRANSFERASE / methyltransferase / polyketide / anthraquinone | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Photorhabdus laumondii subsp. laumondii TTO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Huber, E.M. / Groll, M. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Structure / Year: 2023 Title: A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments. Authors: Huber, E.M. / Kreling, L. / Heinrich, A.K. / Dunnebacke, M. / Pothig, A. / Bode, H.B. / Groll, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8bib.cif.gz | 546.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8bib.ent.gz | 453.6 KB | Display | PDB format |
PDBx/mmJSON format | 8bib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bib_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8bib_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 8bib_validation.xml.gz | 49.1 KB | Display | |
Data in CIF | 8bib_validation.cif.gz | 68.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/8bib ftp://data.pdbj.org/pub/pdb/validation_reports/bi/8bib | HTTPS FTP |
-Related structure data
Related structure data | 8bgtSC 8bgxC 8bgyC 8bgzC 8bh0C 8bicC 8bidC 8bieC 8bifC 8bigC 8bihC 8biiC 8bijC 8birC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 36550.527 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus laumondii subsp. laumondii TTO1 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6L9JR93 |
---|
-Non-polymers , 7 types, 507 molecules
#2: Chemical | ChemComp-SAH / #3: Chemical | ChemComp-QOI / #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-CO3 / #6: Chemical | ChemComp-GOL / | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M NaI, 0.1 M bis-tris propane pH 6.5, 20% PEG3350 |
-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: Apr 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48 Å / Num. obs: 68830 / % possible obs: 96.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.3→2.4 Å / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2 / Num. unique obs: 8321 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8BGT Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 20.196 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.244 / 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: 276 Å2 / Biso mean: 45.363 Å2 / Biso min: 26.55 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|