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- PDB-9c64: Cytidine deaminase T6S toxin from Pseudomonas syringae complexed ... -

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Basic information

Entry
Database: PDB / ID: 9c64
TitleCytidine deaminase T6S toxin from Pseudomonas syringae complexed with substrate DNA
Components
  • DNA (5'-D(*AP*AP*AP*AP*AP*AP*TP*CP*GP*AP*AP*AP*AP*AP*A)-3')
  • SsdA
KeywordsTOXIN/DNA / toxin / DNA binding / deaminase / TOXIN-DNA complex
Function / homology: / Single-strand DNA deaminase toxin A, C-terminal / Class I prePAAR effector Rhs1 motif / PAAR motif / PAAR motif / membrane / DNA / DNA (> 10) / Rhs protein
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsShi, K. / Yin, L. / Aihara, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA234228 NCI United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for sequence context-independent single-stranded DNA cytosine deamination by the bacterial toxin SsdA.
Authors: Yin, L. / Chen, Y. / Shi, K. / Barreto Duran, E. / Harris, R.S. / Aihara, H.
History
DepositionJun 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 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: SsdA
B: SsdA
C: DNA (5'-D(*AP*AP*AP*AP*AP*AP*TP*CP*GP*AP*AP*AP*AP*AP*A)-3')
D: DNA (5'-D(*AP*AP*AP*AP*AP*AP*TP*CP*GP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6948
Polymers45,4394
Non-polymers2554
Water4,342241
1
A: SsdA
C: DNA (5'-D(*AP*AP*AP*AP*AP*AP*TP*CP*GP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8474
Polymers22,7192
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-35 kcal/mol
Surface area9280 Å2
MethodPISA
2
B: SsdA
D: DNA (5'-D(*AP*AP*AP*AP*AP*AP*TP*CP*GP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8474
Polymers22,7192
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-34 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.919, 87.919, 134.482
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein SsdA


Mass: 18083.240 Da / Num. of mol.: 2 / Mutation: E348A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Q0DAS4
#2: DNA chain DNA (5'-D(*AP*AP*AP*AP*AP*AP*TP*CP*GP*AP*AP*AP*AP*AP*A)-3')


Mass: 4636.104 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pseudomonas syringae (bacteria)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.15M Ammonium Chloride, 22.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.94→66.26 Å / Num. obs: 39004 / % possible obs: 89.7 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.061 / Rrim(I) all: 0.164 / Rsym value: 0.152 / Net I/σ(I): 7.7
Reflection shellResolution: 1.942→2.032 Å / % possible obs: 35.2 % / Redundancy: 7.3 % / Rmerge(I) obs: 1.702 / Num. measured all: 14248 / Num. unique obs: 1950 / Rpim(I) all: 0.674 / Rrim(I) all: 1.832 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→66.26 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1902 1933 4.96 %
Rwork0.1613 --
obs0.1627 38972 89.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→66.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 374 10 241 3007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d16.8061128
X-RAY DIFFRACTIONf_chiral_restr0.067423
X-RAY DIFFRACTIONf_plane_restr0.009454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.2619420.2626546X-RAY DIFFRACTION19
1.99-2.050.2728810.23541814X-RAY DIFFRACTION61
2.05-2.110.2431190.22742468X-RAY DIFFRACTION84
2.11-2.170.2361530.20712799X-RAY DIFFRACTION96
2.17-2.250.26191520.19412930X-RAY DIFFRACTION100
2.25-2.340.21891580.18392917X-RAY DIFFRACTION100
2.34-2.450.23461540.17942951X-RAY DIFFRACTION100
2.45-2.580.21121410.18292944X-RAY DIFFRACTION100
2.58-2.740.21721740.18492915X-RAY DIFFRACTION100
2.74-2.950.22231600.1772922X-RAY DIFFRACTION100
2.95-3.250.19011470.17252946X-RAY DIFFRACTION100
3.25-3.720.18611420.14682948X-RAY DIFFRACTION100
3.72-4.680.14111470.12312960X-RAY DIFFRACTION100
4.68-66.260.14781630.13562979X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.54694.68722.23246.38154.16436.09780.20640.30640.1951-0.8786-0.17680.2557-0.6478-0.3147-0.02910.22020.13190.02120.3593-0.03530.2558-63.049151.56614.2433
27.2967-6.39973.82325.6446-3.07734.2340.52650.1911-1.2333-0.2207-0.60111.65581.6261-1.12950.04440.49910.0012-0.08010.4125-0.16820.5737-60.804828.1827-0.4905
34.9151-1.3025-0.55462.88920.07182.09860.32720.73220.3353-0.7127-0.1612-0.4938-0.15880.1809-0.16030.26280.06640.04630.3692-0.08030.335-48.957140.5394-2.2386
40.96410.3805-0.80844.8483-0.01132.0308-0.1801-0.46810.4530.44470.5016-0.61680.26160.6057-0.29920.23490.1042-0.08680.4006-0.16170.3876-40.524433.94728.4273
53.5195-2.0407-1.34293.05852.26813.01430.0798-0.15460.3446-0.02530.2181-0.353-0.16130.2048-0.23770.17170.02410.0120.2459-0.06420.2911-51.980748.07969.0819
69.32486.1696-3.0437.0021-1.95031.7508-0.21680.42290.1429-0.41010.27550.2275-0.02820.0657-0.04790.3359-0.0205-0.01180.2558-0.06050.2007-23.45117.6853-12.0722
71.26080.38451.79045.7158-5.01768.0524-0.3564-0.3548-0.10920.00910.1012-1.48040.1361.7725-0.33190.3544-0.09310.01180.7452-0.21550.4612-4.482130.9015-6.6868
83.4441-0.4002-0.57241.70110.62234.94820.01680.00660.6061-0.33110.0476-0.0392-0.73740.2517-0.00180.3355-0.0395-0.01340.1927-0.05280.2928-20.128533.6285-2.0138
93.73812.16574.10831.77372.23084.8516-0.1051-0.97510.20770.25340.1813-0.03950.2860.116-0.01610.23410.0872-0.02790.4607-0.10110.2311-18.302527.236612.2109
104.62771.66885.19322.97733.60727.1245-0.0939-0.42260.2838-0.2840.4065-0.1536-0.25310.8187-0.22820.2338-0.02610.03440.4366-0.17070.2749-15.451132.83389.3104
112.3259-0.0015-0.35633.66610.81052.1131-0.0723-0.0569-0.0951-0.04730.10050.01110.05020.1307-0.03410.2160.0251-0.01660.2137-0.04010.1729-25.158819.1646-0.4769
122.4999-1.185-0.40924.15250.55987.2167-0.1167-0.3703-2.35920.35530.3043-0.03592.1926-0.60770.2090.8268-0.0377-0.05870.414-0.14641.1466-50.332122.4963.8737
133.16262.72683.33398.23950.69264.56930.4788-1.31620.55880.9458-0.151-1.7779-0.29131.93220.05440.4577-0.1879-0.03691.0684-0.29810.7789-4.776131.82846.1398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 255 through 279 )
2X-RAY DIFFRACTION2chain 'A' and (resid 280 through 289 )
3X-RAY DIFFRACTION3chain 'A' and (resid 290 through 325 )
4X-RAY DIFFRACTION4chain 'A' and (resid 326 through 340 )
5X-RAY DIFFRACTION5chain 'A' and (resid 341 through 408 )
6X-RAY DIFFRACTION6chain 'B' and (resid 255 through 279 )
7X-RAY DIFFRACTION7chain 'B' and (resid 280 through 289 )
8X-RAY DIFFRACTION8chain 'B' and (resid 290 through 324 )
9X-RAY DIFFRACTION9chain 'B' and (resid 325 through 334 )
10X-RAY DIFFRACTION10chain 'B' and (resid 335 through 346 )
11X-RAY DIFFRACTION11chain 'B' and (resid 347 through 408 )
12X-RAY DIFFRACTION12chain 'C' and (resid -3 through 6 )
13X-RAY DIFFRACTION13chain 'D' and (resid -3 through 4 )

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