+Open data
-Basic information
Entry | Database: PDB / ID: 8k5q | ||||||
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Title | Crystal structure of YajQ STM0435 with c-di-GMP | ||||||
Components | YajQ | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Dai, Y. / Zhang, M. / Wang, W. / Li, B. | ||||||
Funding support | China, 1items
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Citation | Journal: Virulence / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k5q.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k5q.ent.gz | 62.5 KB | Display | PDB format |
PDBx/mmJSON format | 8k5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k5q_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8k5q_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8k5q_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 8k5q_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/8k5q ftp://data.pdbj.org/pub/pdb/validation_reports/k5/8k5q | HTTPS FTP |
-Related structure data
Related structure data | 8k4iC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria) Gene: yajQ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A636K9V1 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.76 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→31.57 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.26 / Stereochemistry target values: ML
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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: 2.28→31.57 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: 7.5244 Å / Origin y: 2.7785 Å / Origin z: 0.9405 Å
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Refinement TLS group | Selection details: all |