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- PDB-9owg: Crystal Structure of the Immunity Protein (52 domain-containing p... -

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Basic information

Entry
Database: PDB / ID: 9owg
TitleCrystal Structure of the Immunity Protein (52 domain-containing protein) from Pseudomonas aeruginosa PAO1.
ComponentsImmunity protein 52 domain-containing protein
KeywordsANTITOXIN / 52 domain-containing protein / CSBID / Structural Genomics / Center for Structural Biology of Infectious Diseases
Function / homologyImm52 family, TsiT-like / Immunity protein 52 / Immunity protein 52 / CARBONATE ION / PHOSPHATE ION / Immunity protein 52 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMinasov, G. / Wawrzak, Z. / Skarina, T. / Stogios, P.J. / Savchenko, A. / Satchell, K.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
CitationJournal: To Be Published
Title: Crystal Structure of the Immunity Protein (52 domain-containing protein) from Pseudomonas aeruginosa PAO1.
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Stogios, P.J. / Savchenko, A. / Satchell, K.F. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionJun 2, 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

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Assembly

Deposited unit
A: Immunity protein 52 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1526
Polymers27,6011
Non-polymers5505
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.425, 86.425, 81.853
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Immunity protein 52 domain-containing protein


Mass: 27601.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA3908 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Magic / References: UniProt: Q9HXA5

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Non-polymers , 5 types, 105 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 8.5 mg/ml, 0.3M Sodium chloride, 0.01M HEPES (pH 7.5); Screen: 0.15M Sodium dihydrogen phosphate, 20% (w/v) PEG 3350; Cryo: glycerol, paratone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.27815 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27815 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 26908 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 34.9 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.017 / Rrim(I) all: 0.054 / Rsym value: 0.052 / Χ2: 1.013 / Net I/σ(I): 42.6
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1251 / CC1/2: 0.66 / CC star: 0.892 / Rpim(I) all: 0.39 / Χ2: 1.004 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→27.62 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 5.433 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20051 1226 4.6 %RANDOM
Rwork0.17168 ---
obs0.17294 25678 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.336 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20.41 Å2-0 Å2
2--0.81 Å20 Å2
3----2.63 Å2
Refinement stepCycle: 1 / Resolution: 1.65→27.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 33 100 1969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121955
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161820
X-RAY DIFFRACTIONr_angle_refined_deg1.431.6492663
X-RAY DIFFRACTIONr_angle_other_deg0.7911.574184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1135236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.08521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.03510309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022337
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02475
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7532.786935
X-RAY DIFFRACTIONr_mcbond_other2.7532.785935
X-RAY DIFFRACTIONr_mcangle_it3.8134.9851174
X-RAY DIFFRACTIONr_mcangle_other3.8154.9881175
X-RAY DIFFRACTIONr_scbond_it4.4223.4961020
X-RAY DIFFRACTIONr_scbond_other4.3763.4911018
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6266.1221487
X-RAY DIFFRACTIONr_long_range_B_refined9.89332.832213
X-RAY DIFFRACTIONr_long_range_B_other9.90331.762193
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 74 -
Rwork0.328 1792 -
obs--91.16 %
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)
10.5606-1.2799-0.0183.08450.67582.69550.02630.0351-0.1027-0.0658-0.14530.25960.159-0.21250.1190.0888-0.07420.02920.2137-0.08460.176219.84928.72420.633
21.6307-2.47620.17753.93060.39122.8256-0.2284-0.0026-0.34470.4711-0.08180.56680.5612-0.54090.31020.1852-0.14990.11920.2375-0.14980.298415.93525.62324.896
31.6314-0.154-1.49911.0410.24873.0544-0.06260.0756-0.05770.0289-0.08350.0258-0.10940.06040.14610.038-0.0505-0.00110.1125-0.02790.080226.10538.97627.33
43.0443-0.6748-2.57571.91261.27864.63540.27480.02640.1599-0.0219-0.15370.0052-0.60220.2582-0.1210.132-0.07530.00980.0785-0.01510.040125.94449.92329.837
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 68
2X-RAY DIFFRACTION2A69 - 119
3X-RAY DIFFRACTION3A120 - 168
4X-RAY DIFFRACTION4A169 - 238

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