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- PDB-9nlg: CBASS Pseudomonas syringae Cap5 tetramer with 3'2'-c-GAMP cyclic ... -

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Basic information

Entry
Database: PDB / ID: 9nlg
TitleCBASS Pseudomonas syringae Cap5 tetramer with 3'2'-c-GAMP cyclic dinucleotide ligand (His56Ala mutant without Mg2+ ions)
ComponentsHNH endonuclease
KeywordsIMMUNE SYSTEM / Bacterial immunity / CBASS / cyclic dinucleotide / Cap5 effector DNA endonuclease / viral defense / DNA
Function / homologyHNH endonuclease / SMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / HNH nuclease / metal ion binding / 3'2'-cGAMP / HNH endonuclease
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsRechkoblit, O. / Aggarwal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM131780 United States
CitationJournal: Nat Commun / Year: 2025
Title: Mechanism of DNA degradation by CBASS Cap5 endonuclease immune effector.
Authors: Rechkoblit, O. / Sciaky, D. / Ni, M. / Li, Y. / Kottur, J. / Fang, G. / Aggarwal, A.K.
History
DepositionMar 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HNH endonuclease
B: HNH endonuclease
C: HNH endonuclease
D: HNH endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,86013
Polymers170,8094
Non-polymers3,0519
Water27,0231500
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Mass photometry (Refeyn)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18780 Å2
ΔGint-44 kcal/mol
Surface area54340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.564, 77.833, 80.989
Angle α, β, γ (deg.)63.400, 80.840, 79.170
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
HNH endonuclease


Mass: 42702.168 Da / Num. of mol.: 4 / Mutation: H56A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2P0QGK5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-4UR / 3'2'-cGAMP / 2-amino-9-[(2S,5R,7R,8R,10R,12aR,14R,15R,15aS,16R)-7-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxy-2,10-dioxidooctahydro-12H-5,8-methanofuro[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecin-14-yl]-1,9-dihydro-6H-purin-6-one


Mass: 674.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1500 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 10 mM Trisodiumcitrate pH 9.0, 28% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 1.64→69.054 Å / Num. obs: 173836 / % possible obs: 94.7 % / Redundancy: 2.8 % / Biso Wilson estimate: 18.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.3
Reflection shellResolution: 1.64→1.683 Å / Rmerge(I) obs: 0.547 / Num. unique obs: 8697 / CC1/2: 0.687

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCBUILT 20220820data reduction
autoPROCBUILT 20220820data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→45.87 Å / SU ML: 0.1854 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 17.2105
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1806 8587 4.94 %
Rwork0.156 165231 -
obs0.1572 173818 94.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.85 Å2
Refinement stepCycle: LAST / Resolution: 1.64→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11287 0 190 1500 12977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004711832
X-RAY DIFFRACTIONf_angle_d0.773516172
X-RAY DIFFRACTIONf_chiral_restr0.04741803
X-RAY DIFFRACTIONf_plane_restr0.01232136
X-RAY DIFFRACTIONf_dihedral_angle_d14.31234483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.660.3261240.30642613X-RAY DIFFRACTION44.91
1.66-1.680.31172650.26245331X-RAY DIFFRACTION90.76
1.68-1.70.2822690.24735498X-RAY DIFFRACTION94.87
1.7-1.720.27742860.24125649X-RAY DIFFRACTION95.69
1.72-1.750.26032880.22395523X-RAY DIFFRACTION95.56
1.75-1.770.24092820.20435571X-RAY DIFFRACTION95.78
1.77-1.80.20513220.19285519X-RAY DIFFRACTION95.91
1.8-1.820.20393190.1785587X-RAY DIFFRACTION95.91
1.82-1.850.20892880.17335610X-RAY DIFFRACTION96.06
1.85-1.880.20893020.17865556X-RAY DIFFRACTION96.19
1.88-1.910.21322980.16675618X-RAY DIFFRACTION96.38
1.91-1.950.19232800.16625630X-RAY DIFFRACTION96.22
1.95-1.990.18563080.16195598X-RAY DIFFRACTION96.46
1.99-2.030.20042980.1685627X-RAY DIFFRACTION96.51
2.03-2.070.1872890.16735625X-RAY DIFFRACTION96.76
2.07-2.120.20092940.15865645X-RAY DIFFRACTION96.98
2.12-2.170.17783090.14565612X-RAY DIFFRACTION96.88
2.17-2.230.17373190.14495616X-RAY DIFFRACTION96.85
2.23-2.30.1892720.14555671X-RAY DIFFRACTION96.79
2.3-2.370.17962700.1475656X-RAY DIFFRACTION96.72
2.37-2.450.1782860.15185638X-RAY DIFFRACTION96.45
2.45-2.550.17113070.14815612X-RAY DIFFRACTION97.14
2.55-2.670.1762610.15285648X-RAY DIFFRACTION96.55
2.67-2.810.18353210.15385673X-RAY DIFFRACTION97.15
2.81-2.990.20542950.14985663X-RAY DIFFRACTION97.4
2.99-3.220.16932700.14765681X-RAY DIFFRACTION97.19
3.22-3.540.15362730.13915682X-RAY DIFFRACTION97.19
3.54-4.050.14632800.13135624X-RAY DIFFRACTION96.64
4.05-5.10.14063170.12045606X-RAY DIFFRACTION96.73
5.1-45.870.1762950.17925649X-RAY DIFFRACTION96.9

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