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

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Basic information

Entry
Database: PDB / ID: 9dif
TitleCBASS Pseudomonas syringae Cap5 tetramer with DNA duplex and 3'2'-c-GAMP 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 / 3'2'-cGAMP / DNA / DNA (> 10) / HNH endonuclease
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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)92,7047
Polymers91,2243
Non-polymers1,4804
Water11,998666
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)185,40814
Polymers182,4486
Non-polymers2,9598
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area22000 Å2
ΔGint-80 kcal/mol
Surface area61030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.021, 194.171, 118.626
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-795-

HOH

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Components

#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)
#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.: 2 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 3.31 Å3/Da / Density % sol: 62.89 % / Description: Rod-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 10 mM tri-sodium citrate titrated to pH 9.0; 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: 0.920105 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 1.67→97.086 Å / Num. obs: 69262 / % possible obs: 94.3 % / Redundancy: 8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.152 / Net I/σ(I): 8.5
Reflection shellResolution: 1.67→1.941 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3464 / CC1/2: 0.598 / % possible all: 70.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSJan 10, 2022 (BUILT 20220820)data reduction
Aimless0.7.7data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→39.32 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 3404 4.92 %
Rwork0.1698 --
obs0.1718 69237 49.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5674 386 92 669 6821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156784
X-RAY DIFFRACTIONf_angle_d1.2839416
X-RAY DIFFRACTIONf_dihedral_angle_d19.0252614
X-RAY DIFFRACTIONf_chiral_restr0.0671051
X-RAY DIFFRACTIONf_plane_restr0.0171105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.690.768820.353850X-RAY DIFFRACTION1
1.7-1.720.317950.389487X-RAY DIFFRACTION2
1.72-1.750.298780.3207132X-RAY DIFFRACTION2
1.75-1.780.4680.372185X-RAY DIFFRACTION3
1.78-1.810.506380.3203263X-RAY DIFFRACTION5
1.81-1.840.3945220.3186399X-RAY DIFFRACTION7
1.84-1.870.3475370.3058651X-RAY DIFFRACTION12
1.87-1.910.346370.2828860X-RAY DIFFRACTION15
1.91-1.950.3175550.24881001X-RAY DIFFRACTION18
1.95-20.25630.24471227X-RAY DIFFRACTION22
2-2.050.2558820.22971512X-RAY DIFFRACTION28
2.05-2.110.2423890.20891773X-RAY DIFFRACTION32
2.11-2.170.23871310.21172164X-RAY DIFFRACTION40
2.17-2.240.24181420.20762686X-RAY DIFFRACTION49
2.24-2.320.27731960.20343579X-RAY DIFFRACTION65
2.32-2.410.2172480.20614573X-RAY DIFFRACTION83
2.41-2.520.23932920.20895406X-RAY DIFFRACTION98
2.52-2.650.22322570.19375563X-RAY DIFFRACTION100
2.65-2.820.22882890.1825555X-RAY DIFFRACTION100
2.82-3.040.21713330.17425502X-RAY DIFFRACTION100
3.04-3.340.21382800.15625580X-RAY DIFFRACTION100
3.34-3.820.18962440.1415632X-RAY DIFFRACTION100
3.82-4.820.1612700.12225659X-RAY DIFFRACTION100
4.82-39.320.20243060.17355794X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -15.9018 Å / Origin y: -37.8769 Å / Origin z: -25.4476 Å
111213212223313233
T-0.0373 Å20.0635 Å20.0299 Å2-0.1146 Å2-0.0058 Å2--0.0539 Å2
L0.8624 °20.4385 °20.3543 °2-1.0413 °20.4029 °2--1.6816 °2
S-0.0501 Å °-0.0833 Å °0.0317 Å °-0.0444 Å °0.0001 Å °0.0329 Å °-0.1839 Å °-0.2923 Å °0.008 Å °
Refinement TLS groupSelection details: all

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