[English] 日本語
Yorodumi- PDB-7w07: Itaconate inducible LysR-Type Transcriptional regulator (ITCR) in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w07 | ||||||
---|---|---|---|---|---|---|---|
Title | Itaconate inducible LysR-Type Transcriptional regulator (ITCR) in complex with itaconate, Space group C121. | ||||||
Components | Transcriptional regulator, LysR family | ||||||
Keywords | TRANSCRIPTION / LTTR / ITCR / itaconate | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Yersinia pseudotuberculosis serotype O:3 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Sun, P.K. / Wang, B. / Li, X.J. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2022 Title: A genetically encoded fluorescent biosensor for detecting itaconate with subcellular resolution in living macrophages. Authors: Sun, P. / Zhang, Z. / Wang, B. / Liu, C. / Chen, C. / Liu, P. / Li, X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7w07.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7w07.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 7w07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w07_validation.pdf.gz | 455 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7w07_full_validation.pdf.gz | 456.6 KB | Display | |
Data in XML | 7w07_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 7w07_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/7w07 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/7w07 | HTTPS FTP |
-Related structure data
Related structure data | 7w06SC 7w08C S: Starting model for refinement 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
#1: Protein | Mass: 32258.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pseudotuberculosis serotype O:3 (strain YPIII) (bacteria) Strain: YPIII / Gene: YPK_2265 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3B558 |
---|---|
#2: Chemical | ChemComp-ITN / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.45 Å3/Da / Density % sol: 15.36 % |
---|---|
Crystal grow | Temperature: 276 K / Method: evaporation Details: 1.6M Ammonium sulfate, 0.1M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Mar 10, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.48→42.57 Å / Num. obs: 27190 / % possible obs: 87.3 % / Redundancy: 12.4 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.014 / Rrim(I) all: 0.052 / Net I/σ(I): 27 / Num. measured all: 338461 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7W06 Resolution: 1.48→41.1 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.31 / 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: 49.73 Å2 / Biso mean: 23.4514 Å2 / Biso min: 12.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.48→41.1 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
|