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Open data
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Basic information
Entry | Database: PDB / ID: 8k4i | ||||||
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Title | Crystal structure of YajQ STM0435 | ||||||
![]() | YajQ | ||||||
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Function / homology | Protein of unknown function DUF520 / UPF0234, N-terminal / YajQ-like superfamily / Protein of unknown function (DUF520) / UPF0234-like, C-terminal / UPF0234 protein YajQ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dai, Y. / Zhang, M. / Wang, W. / Li, B. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.6 KB | Display | ![]() |
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PDB format | ![]() | 61.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8k5qC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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: ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.53 % |
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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 |
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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![]() |
Reflection | Resolution: 1.48→39.5 Å / Num. obs: 23099 / % possible obs: 87.3 % / Redundancy: 9.1 % / CC1/2: 1 / Net I/σ(I): 33.8 |
Reflection shell | Resolution: 1.48→1.56 Å / Num. unique obs: 1748 / CC1/2: 0.917 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→32.93 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 5.652 Å / Origin y: -1.5997 Å / Origin z: -2.3513 Å
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Refinement TLS group | Selection details: all |