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- PDB-9dih: CBASS Pseudomonas syringae Cap5 tetramer with DNA duplex and 3'2'... -

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Basic information

Entry
Database: PDB / ID: 9dih
TitleCBASS Pseudomonas syringae Cap5 tetramer with DNA duplex and 3'2'-c-diAMP cyclic dinucleotide ligand
Components
  • DNA (5'-D(*TP*TP*GP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*CP*A)-3')
  • HNH endonuclease
KeywordsIMMUNE SYSTEM / Bacterial immunity / CBASS / cyclic dinucleotide / Cap5 effector DNA endonuclease / viral defense / HNH endonuclease / 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 / : / DNA / DNA (> 10) / HNH endonuclease
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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
DepositionSep 5, 2024Deposition 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
D: DNA (5'-D(*TP*TP*GP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7648
Polymers91,2243
Non-polymers1,5405
Water7,260403
1
A: HNH endonuclease
B: HNH endonuclease
D: DNA (5'-D(*TP*TP*GP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*CP*A)-3')
hetero molecules

A: HNH endonuclease
B: HNH endonuclease
D: DNA (5'-D(*TP*TP*GP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,52816
Polymers182,4486
Non-polymers3,07910
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area22840 Å2
ΔGint-78 kcal/mol
Surface area61380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.697, 191.527, 118.435
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-11-

DA

21A-694-

HOH

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Components

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Protein / DNA chain , 2 types, 3 molecules ABD

#1: Protein HNH endonuclease


Mass: 42702.168 Da / Num. of mol.: 2 / Mutation: H56A
Source method: isolated from a genetically manipulated source
Details: This protein features a mutation at a catalytic residue; specifically, His56 in the wild-type protein has been replaced with Ala56 to prevent DNA degradation during crystallization.
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2P0QGK5
#2: DNA chain DNA (5'-D(*TP*TP*GP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*CP*A)-3')


Mass: 5819.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 408 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-Y4F / Cyclic (adenosine-(2'-5')-monophosphate-adenosine-(3'-5')-monophosphate


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.22 Å3/Da / Density % sol: 61.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 10 mM tri-sodium citrate titrated to pH 9.0 and 26-30% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920085 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920085 Å / Relative weight: 1
ReflectionResolution: 1.94→95.763 Å / Num. obs: 57760 / % possible obs: 94.7 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.8
Reflection shellResolution: 1.94→2.181 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2890 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→47.88 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 1963 3.4 %
Rwork0.1705 --
obs0.1722 57729 66.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5753 386 96 405 6640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0176859
X-RAY DIFFRACTIONf_angle_d1.5429516
X-RAY DIFFRACTIONf_dihedral_angle_d19.6252636
X-RAY DIFFRACTIONf_chiral_restr0.0731062
X-RAY DIFFRACTIONf_plane_restr0.021120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.479440.308576X-RAY DIFFRACTION1
1.99-2.050.4562100.3095351X-RAY DIFFRACTION6
2.05-2.110.3016290.2585770X-RAY DIFFRACTION13
2.11-2.180.206520.24891460X-RAY DIFFRACTION25
2.18-2.250.2994670.22572160X-RAY DIFFRACTION36
2.25-2.340.27571150.21993468X-RAY DIFFRACTION59
2.34-2.450.28362000.22375421X-RAY DIFFRACTION91
2.45-2.580.27752030.20945934X-RAY DIFFRACTION100
2.58-2.740.22892080.19465942X-RAY DIFFRACTION100
2.74-2.950.25292160.19555956X-RAY DIFFRACTION100
2.95-3.250.21622130.18265972X-RAY DIFFRACTION100
3.25-3.720.2422110.15616000X-RAY DIFFRACTION100
3.72-4.690.16782140.136043X-RAY DIFFRACTION100
4.69-47.880.20052210.16496213X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -15.3689 Å / Origin y: -37.3652 Å / Origin z: -24.9238 Å
111213212223313233
T0.168 Å20.0467 Å20.016 Å2-0.2076 Å2-0.0005 Å2--0.1939 Å2
L0.8806 °20.3109 °20.223 °2-0.8395 °20.2883 °2--1.2523 °2
S-0.0645 Å °-0.0649 Å °0.0825 Å °-0.0389 Å °0.0086 Å °0.0299 Å °-0.1953 Å °-0.1711 Å °0.0298 Å °
Refinement TLS groupSelection details: all

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