+Open data
-Basic information
Entry | Database: PDB / ID: 6wp9 | ||||||
---|---|---|---|---|---|---|---|
Title | AvaR1 bound to Avenolide | ||||||
Components | AvaR1 | ||||||
Keywords | DNA BINDING PROTEIN/HORMONE / Transcriptional Repressor bound ligand / DNA BINDING PROTEIN / DNA BINDING PROTEIN-INHIBITOR complex / DNA BINDING PROTEIN-HORMONE complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avermitilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kapoor, I. / Olivares, P.J. / Nair, S.K. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Elife / Year: 2020 Title: Biochemical basis for the regulation of biosynthesis of antiparasitics by bacterial hormones. Authors: Kapoor, I. / Olivares, P. / Nair, S.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6wp9.cif.gz | 366.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6wp9.ent.gz | 296.3 KB | Display | PDB format |
PDBx/mmJSON format | 6wp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wp9_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6wp9_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 6wp9_validation.xml.gz | 75.2 KB | Display | |
Data in CIF | 6wp9_validation.cif.gz | 105.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/6wp9 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/6wp9 | HTTPS FTP |
-Related structure data
Related structure data | 6wp7SC 6wpaC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26989.590 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: Transcriptional Inhibitor / Source: (gene. exp.) Streptomyces avermitilis (bacteria) Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680 Gene: avaR1, SAVERM_3705 / Plasmid: Rosetta Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q82H41 #2: Chemical | ChemComp-XVR / ( #3: 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: 2.19 Å3/Da / Density % sol: 43.72 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 23% PEG3350 and 0.1M sodium acetate trihydrate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 116595 / % possible obs: 97.83 % / Redundancy: 4.8 % / CC1/2: 0.992 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2→2.07 Å / Num. unique obs: 11301 / CC1/2: 0.998 / % possible all: 95.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WP7 Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.377 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.18 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.39 Å2 / Biso mean: 23.637 Å2 / Biso min: 2.1 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→25 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|