[English] 日本語
Yorodumi- PDB-5t81: Rhombohedral crystal form of the EpoB NRPS cyclization-docking bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t81 | ||||||
---|---|---|---|---|---|---|---|
Title | Rhombohedral crystal form of the EpoB NRPS cyclization-docking bidomain from Sorangium cellulosum | ||||||
Components | EpoB | ||||||
Keywords | BIOSYNTHETIC PROTEIN / epothilone / NRPS / thiazoline / cyclization | ||||||
Function / homology | Function and homology information organic substance biosynthetic process / phosphopantetheine binding / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Sorangium cellulosum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.604 Å | ||||||
Authors | Dowling, D.P. / Kung, Y. / Croft, A.K. / Taghizadeh, K. / Kelly, W.L. / Walsh, C.T. / Drennan, C.L. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Structural elements of an NRPS cyclization domain and its intermodule docking domain. Authors: Dowling, D.P. / Kung, Y. / Croft, A.K. / Taghizadeh, K. / Kelly, W.L. / Walsh, C.T. / Drennan, C.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5t81.cif.gz | 214.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5t81.ent.gz | 171.6 KB | Display | PDB format |
PDBx/mmJSON format | 5t81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/5t81 ftp://data.pdbj.org/pub/pdb/validation_reports/t8/5t81 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 61764.223 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sorangium cellulosum (bacteria) / Gene: epoB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KIZ9 #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | Sequence details | NcoI restriction site was used for the original cloning into pET30a, introducing an Ala ...NcoI restriction site was used for the original cloning into pET30a, introducing an Ala substitution for Thr at position two | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.88 % / Description: Rhombohedral crystals formed after 4 weeks. |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: reservoir of 56% tacsimate (pH 7.0; Hampton Research, Aliso Viejo, CA) and 1% PEG 1,500 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97946 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 47986 / % possible obs: 99.7 % / Redundancy: 3 % / Rsym value: 0.062 / Net I/σ(I): 40.5 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3.4 / % possible all: 99.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2.604→43.732 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.17
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.98 Å2 / Biso mean: 53.3089 Å2 / Biso min: 29.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.604→43.732 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
|