+
Open data
-
Basic information
Entry | Database: PDB / ID: 8k5q | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of YajQ STM0435 with c-di-GMP | ||||||
![]() | YajQ | ||||||
![]() | STRUCTURAL GENOMICS | ||||||
Function / homology | Protein of unknown function DUF520 / UPF0234, N-terminal / YajQ-like superfamily / Protein of unknown function (DUF520) / UPF0234-like, C-terminal / Chem-C2E / UPF0234 protein YajQ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dai, Y. / Zhang, M. / Wang, W. / Li, B. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: A c-di-GMP binding effector STM0435 modulates flagellar motility and pathogenicity in Salmonella Authors: Dai , Y. / Liu , R. / Yue , Y. / Song , N. / Jia , H. / Ma , Z. / Gao , X. / Zhang , M. / Yuan , X. / Liu , Q. / Liu , X. / Li , B. / Wang , W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 84.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 62.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k4iC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 18344.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: yajQ / Production host: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.76 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.2M Lithium acetate dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 2, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→126.27 Å / Num. obs: 8194 / % possible obs: 95.1 % / Redundancy: 12.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.031 / Rrim(I) all: 0.113 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.28→2.42 Å / Num. unique obs: 983 / CC1/2: 0.966 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→31.57 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 7.5244 Å / Origin y: 2.7785 Å / Origin z: 0.9405 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |