[English] 日本語
Yorodumi- PDB-8fmf: Structure of CBASS Cap5 from Pseudomonas syringae as an activated... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fmf | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of CBASS Cap5 from Pseudomonas syringae as an activated tetramer with the cyclic dinucleotide 3'2'-c-diAMP ligand (1 tetramer in the AU) | ||||||
Components | SAVED domain-containing protein | ||||||
Keywords | IMMUNE SYSTEM / cyclic dinucleotide / bacterial immunity / CBASS / Cap5 effector DNA endonuclease / viral defense | ||||||
Function / homology | HNH endonuclease / SMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / HNH nuclease / metal ion binding / dodecaethylene glycol monomethyl ether / : / HNH endonuclease Function and homology information | ||||||
Biological species | Pseudomonas syringae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Rechkoblit, O. / Kreitler, D.F. / Aggarwal, A.K. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2024 Title: Activation of CBASS Cap5 endonuclease immune effector by cyclic nucleotides. Authors: Rechkoblit, O. / Sciaky, D. / Kreitler, D.F. / Buku, A. / Kottur, J. / Aggarwal, A.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8fmf.cif.gz | 1003.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8fmf.ent.gz | 702.4 KB | Display | PDB format |
PDBx/mmJSON format | 8fmf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fmf_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8fmf_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 8fmf_validation.xml.gz | 55.2 KB | Display | |
Data in CIF | 8fmf_validation.cif.gz | 76.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/8fmf ftp://data.pdbj.org/pub/pdb/validation_reports/fm/8fmf | HTTPS FTP |
-Related structure data
Related structure data | 8fm1C 8fmgC 8fmhC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 42769.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2P0QGK5 |
---|
-Non-polymers , 7 types, 476 molecules
#2: Chemical | ChemComp-Y4F / Mass: 658.412 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N10O12P2 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-RWB / | #5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-P6G / | #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.03 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris, pH 5.5-6.0, 0.2 M magnesium chloride, 19-20% PEG3350 PH range: 5.5-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→133.987 Å / Num. obs: 64199 / % possible obs: 94.8 % / Redundancy: 12 % / Biso Wilson estimate: 31.68 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.251 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.1→2.32 Å / Rmerge(I) obs: 1.961 / Num. unique obs: 3211 / CC1/2: 0.595 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→66.99 Å / SU ML: 0.2528 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7582 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→66.99 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -29.706 Å / Origin y: 46.86 Å / Origin z: 32.941 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|