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- PDB-8jzl: CryoEM structure of the Salmonella effector inositol phosphate ph... -

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Basic information

Entry
Database: PDB / ID: 8jzl
TitleCryoEM structure of the Salmonella effector inositol phosphate phosphatase SopB
ComponentsInositol phosphate phosphatase SopB
KeywordsLIPID BINDING PROTEIN / Type III secretion system / inositol phosphate phosphatase / bacteria effector
Function / homology
Function and homology information


negative regulation of signaling / symbiont-containing vacuole / lipid phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / regulation of protein kinase activity / positive regulation of DNA replication / molecular function activator activity / cell periphery / negative regulation of cell growth
Similarity search - Function
Phosphatase IpgD/SopB / Enterobacterial virulence protein IpgD
Similarity search - Domain/homology
Inositol phosphate phosphatase SopB
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsJiang, W.X. / Cheng, X.Q. / Wu, M. / Ma, L.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
CitationJournal: To Be Published
Title: CryoEM structure of the Salmonella effector inositol phosphate phosphatase SopB
Authors: Jiang, W.X. / Cheng, X.Q. / Wu, M. / Ma, L.X. / Xing, Q.
History
DepositionJul 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol phosphate phosphatase SopB
B: Inositol phosphate phosphatase SopB
C: Inositol phosphate phosphatase SopB
D: Inositol phosphate phosphatase SopB
E: Inositol phosphate phosphatase SopB
F: Inositol phosphate phosphatase SopB


Theoretical massNumber of molelcules
Total (without water)330,3166
Polymers330,3166
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 64 - 561 / Label seq-ID: 1 - 498

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF

NCS oper:
IDCodeMatrixVector
1given(-0.499882745229, -0.866093083488, 0.000108427577219), (0.866093051754, -0.499882756417, -0.000235670311664), (0.000258313503088, -2.38991511163E-5, 0.999999966351)172.257798903, 27.4724704262, -0.0220970758051
2given(-0.500107316917, 0.865963296165, 0.000491182304885), (-0.865963193328, -0.5001075208, 0.000464154608698), (0.000647584819635, -0.000193218681254, 0.99999977165)62.3318469419, 162.914144915, -0.0387253248703
3given(-0.999999859993, 9.1167194492E-5, 0.00052125077187), (9.11641291908E-5, 0.999999995827, -5.9044217242E-6), (-0.000521251307984, -5.85690152484E-6, -0.999999864131)156.376986986, -0.00851175192321, 124.710603874
4given(0.500442312929, 0.865769828572, -0.000308811255429), (0.865769803912, -0.500442388088, -0.000250677412582), (-0.000371571182654, -0.000141909875907, -0.999999920898)-15.8632697144, 27.547072812, 124.708476123
5given(0.499958687244, -0.866049188532, -0.000337775414112), (-0.866049073483, -0.499958796876, 0.000451381732919), (-0.000559792573166, 6.68578658006E-5, -0.999999841081)94.079426173, 162.908198792, 124.704963231

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Components

#1: Protein
Inositol phosphate phosphatase SopB / Effector protein SopB


Mass: 55052.680 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Gene: sopB, sigD, STM1091 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O30916, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homohexamer of inositol phosphate phosphatase SopB / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 39 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 241912 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 134.99 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008523628
ELECTRON MICROSCOPYf_angle_d0.646331944
ELECTRON MICROSCOPYf_chiral_restr0.04543546
ELECTRON MICROSCOPYf_plane_restr0.00324164
ELECTRON MICROSCOPYf_dihedral_angle_d9.14393138
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints0.0007102396725
ens_1d_3AAELECTRON MICROSCOPYNCS constraints0.000713808770802
ens_1d_4AAELECTRON MICROSCOPYNCS constraints0.000707414130574
ens_1d_5AAELECTRON MICROSCOPYNCS constraints0.000712458460239
ens_1d_6AAELECTRON MICROSCOPYNCS constraints0.000708337389142

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