+Open data
-Basic information
Entry | Database: PDB / ID: 7eqe | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of a transcription factor | ||||||
Components | TetR/AcrR family transcriptional regulator | ||||||
Keywords | TRANSCRIPTION / Transcription factor | ||||||
Function / homology | DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / regulation of gene expression / DNA binding / TetR/AcrR family transcriptional regulator Function and homology information | ||||||
Biological species | Streptomyces griseoluteus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / SAD / Resolution: 2.399 Å | ||||||
Authors | Uehara, S. / Tsugita, A. / Matsui, T. / Yokoyama, T. / Ostash, I. / Ostash, B. / Tanaka, Y. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Febs J. / Year: 2022 Title: The carbohydrate tail of landomycin A is responsible for its interaction with the repressor protein LanK. Authors: Tsugita, A. / Uehara, S. / Matsui, T. / Yokoyama, T. / Ostash, I. / Deneka, M. / Yalamanchili, S. / Bennett, C.S. / Tanaka, Y. / Ostash, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7eqe.cif.gz | 141.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7eqe.ent.gz | 115 KB | Display | PDB format |
PDBx/mmJSON format | 7eqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eqe_validation.pdf.gz | 455.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7eqe_full_validation.pdf.gz | 463.1 KB | Display | |
Data in XML | 7eqe_validation.xml.gz | 24 KB | Display | |
Data in CIF | 7eqe_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/7eqe ftp://data.pdbj.org/pub/pdb/validation_reports/eq/7eqe | HTTPS FTP |
-Related structure data
Related structure data | 7eqfC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22335.426 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseoluteus (bacteria) / Gene: E5082_18205 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4Z1DIH6 Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.32 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: HEPES-NaOH, polyethylene glycol 4000, isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.97899 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97899 Å / Relative weight: 1 |
Reflection | Resolution: 2.399→47.943 Å / Num. obs: 65417 / % possible obs: 99.4 % / Redundancy: 3.51 % / Rsym value: 0.132 / Net I/σ(I): 7.39 |
Reflection shell | Resolution: 2.399→2.54 Å / Num. unique obs: 10421 / Rsym value: 0.953 |
-Phasing
Phasing | Method: SAD |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.399→47.943 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.18 / Phase error: 30.36 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 197.57 Å2 / Biso mean: 63.4666 Å2 / Biso min: 24.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.399→47.943 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|