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- PDB-6jdp: the imm52 family protein TsiT (PA3908) from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6jdp
Titlethe imm52 family protein TsiT (PA3908) from Pseudomonas aeruginosa
ComponentsImm52 family protein
KeywordsANTITOXIN / Immunity protein / monomer / T6SS
Function / homologyImm52 family, TsiT-like / Immunity protein 52 / Immunity protein 52 / PHOSPHATE ION / Immunity protein 52 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.601 Å
AuthorsShe, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31700651 China
CitationJournal: Protein Sci. / Year: 2019
Title: Structural characterization of the Imm52 family protein TsiT in Pseudomonas aeruginosa.
Authors: She, Z. / Geng, Z. / Xu, J.H. / Li, Y.H. / Dong, Y.H.
History
DepositionFeb 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Imm52 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0783
Polymers29,9601
Non-polymers1182
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-13 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.960, 86.960, 81.108
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-553-

HOH

21A-556-

HOH

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Components

#1: Protein Imm52 family protein


Mass: 29959.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA3908 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HXA5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 37.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.26 M Sodium phosphate monobasic monohydrate, 0.14 M Potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 30138 / % possible obs: 100 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 19.417
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 1.222 / Num. unique obs: 1610 / CC1/2: 0.637 / Rsym value: 0.752 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.601→21.74 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 22.85
RfactorNum. reflection% reflection
Rfree0.2201 1428 4.74 %
Rwork0.1866 --
obs0.1881 30136 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.601→21.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 6 157 2109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062005
X-RAY DIFFRACTIONf_angle_d0.9252725
X-RAY DIFFRACTIONf_dihedral_angle_d2.4661671
X-RAY DIFFRACTIONf_chiral_restr0.05291
X-RAY DIFFRACTIONf_plane_restr0.005359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6006-1.65780.30661450.26992871X-RAY DIFFRACTION100
1.6578-1.72420.29791600.25992862X-RAY DIFFRACTION100
1.7242-1.80260.28051370.23792867X-RAY DIFFRACTION100
1.8026-1.89760.30511520.23382872X-RAY DIFFRACTION100
1.8976-2.01640.23991310.20812869X-RAY DIFFRACTION100
2.0164-2.1720.21421370.19492885X-RAY DIFFRACTION100
2.172-2.39030.20961670.19152840X-RAY DIFFRACTION100
2.3903-2.73560.23091430.1932868X-RAY DIFFRACTION100
2.7356-3.44430.22631430.18352864X-RAY DIFFRACTION100
3.4443-21.7420.1761130.15752910X-RAY DIFFRACTION100

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