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- PDB-9oz0: Crystal structure of T6SS effector-immunity complex PA3907-PA3908... -

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Basic information

Entry
Database: PDB / ID: 9oz0
TitleCrystal structure of T6SS effector-immunity complex PA3907-PA3908 from Pseudomonas aeruginosa
Components
  • Immunity protein 52 domain-containing protein
  • Tox-REase-5 domain-containing protein
KeywordsUNKNOWN FUNCTION / effector / immunity / complex / type 6 / T6SS / secretion system / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homologyTox-REase-5 domain / Restriction endonuclease fold toxin 5 / Imm52 family, TsiT-like / Immunity protein 52 / Immunity protein 52 / CITRIC ACID / Immunity protein 52 domain-containing protein / Tox-REase-5 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.871 Å
AuthorsStogios, P.J. / Borek, D. / Skarina, T. / Osipiuk, J. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
CitationJournal: To Be Published
Title: Crystal structure of T6SS effector-immunity complex PA3907-PA3908 from Pseudomonas aeruginosa
Authors: Stogios, P.J.
History
DepositionJun 4, 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: Immunity protein 52 domain-containing protein
B: Tox-REase-5 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7484
Polymers48,5312
Non-polymers2162
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-10 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.329, 167.329, 167.329
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Immunity protein 52 domain-containing protein


Mass: 27516.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA3908 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic / References: UniProt: Q9HXA5
#2: Protein Tox-REase-5 domain-containing protein


Mass: 21014.881 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA3907 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic / References: UniProt: Q9HXA6
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.06 Å3/Da / Density % sol: 69.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG3350 25%, KCl 0.1M, NaCl 0.1M, MgCl2 10mM, Hepes 0.1M pH 7.5, 10mM NH4Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.87→30 Å / Num. obs: 18909 / % possible obs: 100 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.029 / Net I/σ(I): 20.2
Reflection shellResolution: 2.87→2.92 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.337 / Mean I/σ(I) obs: 1 / Num. unique obs: 925 / CC1/2: 0.528 / Rpim(I) all: 0.458 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.871→29.58 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2855 944 5 %RANDOM
Rwork0.2277 ---
obs0.2305 18870 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.871→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 14 2 3311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033407
X-RAY DIFFRACTIONf_angle_d0.6864632
X-RAY DIFFRACTIONf_dihedral_angle_d6.7622019
X-RAY DIFFRACTIONf_chiral_restr0.041473
X-RAY DIFFRACTIONf_plane_restr0.005612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.871-3.02170.34671310.32242494X-RAY DIFFRACTION100
3.0217-3.21080.35911320.30732507X-RAY DIFFRACTION100
3.2108-3.45840.32661320.272514X-RAY DIFFRACTION100
3.4584-3.80580.30321330.24792531X-RAY DIFFRACTION100
3.8058-4.3550.32271350.21562540X-RAY DIFFRACTION100
4.355-5.48110.22641360.19572595X-RAY DIFFRACTION100
5.4811-29.580.26741450.21272745X-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)
13.3076-1.4670.20726.3907-0.80684.7765-0.3673-0.3393-0.12381.30711.2837-0.4711-0.8262-0.0996-0.62391.23450.18420.34740.73480.04591.0481-3.9855-7.16345.6572
27.1961-1.97050.15962.84794.17057.6497-0.4502-0.58710.48971.10120.4344-0.0812-0.27060.0754-0.00711.06930.1424-0.02880.51620.1410.75337.7358-15.05546.9121
33.4504-1.9472-0.05713.77763.19723.16230.1487-0.22610.4840.21480.1361-1.28-0.19220.4888-0.19370.89810.0260.00790.61490.09820.848812.1455-10.093639.224
44.01360.67250.40963.0486-0.8261.9086-0.0014-0.18070.52330.77250.01410.6969-0.7665-0.7149-0.02261.0720.08870.20850.52410.20380.8623-0.7523-11.692740.3955
54.29470.73212.05374.6873.72278.64460.07090.05890.04340.49180.74720.4316-0.7079-0.6046-0.66311.09230.19550.39120.91720.30530.9117-5.3139-18.359751.1036
62.348-0.6556-1.26153.62810.72055.65470.1802-0.4510.10750.87530.51880.7577-0.0088-1.1456-0.47761.3370.30280.76561.03270.24861.447-13.6942-6.237747.1299
73.4264-1.26640.37493.67452.95215.9947-0.3055-1.40410.47091.68490.31791.65610.4761-1.8306-0.03541.97130.32370.7771.24120.2691.3151-16.6801-10.925457.6269
81.9840.85260.14481.1008-1.99844.9324-0.7646-0.07320.23621.53620.83011.6342-0.7879-0.9429-0.31471.6250.6051.19481.60860.6432.0794-21.1592-4.66350.5196
98.493-3.5623-3.71865.18814.19854.34450.2285-0.09371.3135-0.16280.1386-0.2829-0.272-0.3636-0.64680.8836-0.01830.00060.7020.02710.705-8.327919.381621.6772
104.37634.15775.44475.18346.37757.9710.55931.2716-1.02662.4344-1.075-0.19891.45623.02410.61711.3502-0.00980.10660.98580.28111.37817.3589-3.574312.738
113.78490.0378-0.98164.4086-2.61723.8069-0.0260.4505-0.471-0.4854-0.1074-0.2960.407-0.16690.07260.5259-0.0174-0.01790.4757-0.04440.5423-3.8007-1.349418.5475
121.7859-1.4387-1.34324.697-1.93473.0306-0.1681-0.0668-0.12830.53260.10930.5989-0.0467-0.55260.05270.4047-0.02760.08850.4324-0.00560.5963-7.9548-3.077526.6547
134.46952.7214-3.56583.1768-0.96193.803-0.5972.1074-0.72350.9339-0.40551.77410.7188-3.83180.51271.2567-0.4483-0.11391.9507-0.08121.3834-17.738-14.806613.1204
140.1178-0.17520.14070.3548-0.15010.14270.5968-5.11080.6386-0.44110.15091.3293-0.03481.2637-1.26991.9984-0.03370.92192.65760.05571.8514-32.846-15.486817.3425
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 119 )
5X-RAY DIFFRACTION5chain 'A' and (resid 120 through 145 )
6X-RAY DIFFRACTION6chain 'A' and (resid 146 through 178 )
7X-RAY DIFFRACTION7chain 'A' and (resid 179 through 214 )
8X-RAY DIFFRACTION8chain 'A' and (resid 215 through 239 )
9X-RAY DIFFRACTION9chain 'B' and (resid 84 through 102 )
10X-RAY DIFFRACTION10chain 'B' and (resid 103 through 113 )
11X-RAY DIFFRACTION11chain 'B' and (resid 114 through 167 )
12X-RAY DIFFRACTION12chain 'B' and (resid 168 through 232 )
13X-RAY DIFFRACTION13chain 'B' and (resid 233 through 243 )
14X-RAY DIFFRACTION14chain 'B' and (resid 244 through 252 )

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