[English] 日本語
Yorodumi- PDB-8qnf: Crystal structure of the Condensation domain TomBC from the Tomay... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qnf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Condensation domain TomBC from the Tomaymycin non-ribosomal peptide synthetase | ||||||
Components | Condensation domain TomBC from the Tomaymycin non-ribosomal peptide synthetase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Non-ribosomal peptide synthetase / Tomaymycin / Condensation | ||||||
Function / homology | FORMIC ACID / : Function and homology information | ||||||
Biological species | Streptomyces regensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Karanth, M. / Schmelz, S. / Kirkpatrick, J. / Krausze, J. / Scrima, A. / Carlomagno, T. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Sci Adv / Year: 2024 Title: The specificity of intermodular recognition in a prototypical nonribosomal peptide synthetase depends on an adaptor domain. Authors: Karanth, M.N. / Kirkpatrick, J.P. / Krausze, J. / Schmelz, S. / Scrima, A. / Carlomagno, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8qnf.cif.gz | 244.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8qnf.ent.gz | 160.6 KB | Display | PDB format |
PDBx/mmJSON format | 8qnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qnf_validation.pdf.gz | 464.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8qnf_full_validation.pdf.gz | 471.9 KB | Display | |
Data in XML | 8qnf_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 8qnf_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/8qnf ftp://data.pdbj.org/pub/pdb/validation_reports/qn/8qnf | HTTPS FTP |
-Related structure data
Related structure data | 8qpyC 8qrxC 8qsxC 8rz6C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59291.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TomBC / Source: (gene. exp.) Streptomyces regensis (bacteria) / Variant: FH6421 / Production host: Escherichia coli (E. coli) |
---|
-Non-polymers , 5 types, 382 molecules
#2: Chemical | ChemComp-FMT / #3: Chemical | #4: Chemical | ChemComp-NA / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 63 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: Protein (stored in 50mM Kpi, 150 mM NaCl, pH 7.0) crystallised at 30mg/mL at 4 degC in 100 mM Tris pH 8.5, 3.5 M NaFormate 25% glycerol used as cryoprotectant. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→19.94 Å / Num. obs: 81329 / % possible obs: 85 % / Redundancy: 4.9 % / Biso Wilson estimate: 30.63 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.43 |
Reflection shell | Resolution: 1.65→1.7 Å / Mean I/σ(I) obs: 2.01 / Num. unique obs: 2759 / CC1/2: 0.694 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.65→19.94 Å / SU ML: 0.1726 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.5679 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→19.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|