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- PDB-5h7y: Structure of immunity protein TplEi of T6SS from Pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 5h7y
TitleStructure of immunity protein TplEi of T6SS from Pseudomonas aeruginosa complexed with "L" peptide
Components(Uncharacterized protein) x 2
KeywordsHYDROLASE INHIBITOR/PEPTIDE / antimicrobial peptide / effector -immunity complex / inhibitor / HYDROLASE INHIBITOR-PEPTIDE complex
Function / homology
Function and homology information


endoplasmic reticulum unfolded protein response / lipid metabolic process / autophagy / host cell endoplasmic reticulum membrane / metal ion binding
Similarity search - Function
Tle cognate immunity protein 4, N-terminal domain / Tle cognate immunity protein 4 N-terminal domain / Tle cognate immunity protein 4, C-terminal domain / Tle cognate immunity protein 4 C-terminal domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Alpha/beta hydrolase / Tle cognate immunity protein 4 C-terminal domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.195 Å
AuthorsGao, X.P. / Mu, Z.X. / Cui, S.
Funding support China, 3items
OrganizationGrant numberCountry
Beijing Natural Science Foundation7154226 China
National Natural Science Foundation of China81401714 China
national natural science foundation of chin81572005 China
CitationJournal: Front Cell Infect Microbiol / Year: 2017
Title: Structure-Based Prototype Peptides Targeting the Pseudomonas aeruginosa Type VI Secretion System Effector as a Novel Antibacterial Strategy
Authors: Gao, X.P. / Mu, Z.X. / Qin, B. / Sun, Y. / Cui, S.
History
DepositionNov 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)45,4202
Polymers45,4202
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-19 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.614, 113.614, 128.131
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-443-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 42315.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA1509 / Plasmid: pDUET / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9I3K3
#2: Protein/peptide Uncharacterized protein


Mass: 3104.562 Da / Num. of mol.: 1 / Fragment: UNP residues 82-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA1510 / Plasmid: pDUET / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9I3K2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.63 Å3/Da / Density meas: 0.01 Mg/m3 / Density % sol: 55.9 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Sodium HEPES, 20%(w/v) PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97876 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2014
RadiationMonochromator: Double Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 2.2→34.13 Å / Num. obs: 25539 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 16.22 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 26.69
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 15 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 5.51 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementResolution: 2.195→32.798 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2219 1294 5.08 %
Rwork0.182 --
obs0.1839 25484 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.195→32.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 0 153 2585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122496
X-RAY DIFFRACTIONf_angle_d1.1883380
X-RAY DIFFRACTIONf_dihedral_angle_d11.3911466
X-RAY DIFFRACTIONf_chiral_restr0.059356
X-RAY DIFFRACTIONf_plane_restr0.008433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1953-2.24010.27081410.23742535X-RAY DIFFRACTION97
2.2401-2.28880.29381350.22662627X-RAY DIFFRACTION99
2.2888-2.34210.22551530.18682630X-RAY DIFFRACTION100
2.3421-2.40060.23011310.19252648X-RAY DIFFRACTION100
2.4006-2.46550.24891420.18072657X-RAY DIFFRACTION100
2.4655-2.5380.25371550.18592595X-RAY DIFFRACTION100
2.538-2.61990.22551510.18232636X-RAY DIFFRACTION100
2.6199-2.71350.20261420.17672644X-RAY DIFFRACTION100
2.7135-2.82210.21741260.1822660X-RAY DIFFRACTION100
2.8221-2.95050.30831400.17822628X-RAY DIFFRACTION100
2.9505-3.10590.20781480.18032640X-RAY DIFFRACTION100
3.1059-3.30030.2281290.18342666X-RAY DIFFRACTION100
3.3003-3.55490.2221450.17342638X-RAY DIFFRACTION100
3.5549-3.91210.21661620.17022604X-RAY DIFFRACTION100
3.9121-4.47690.20861550.16692623X-RAY DIFFRACTION100
4.4769-5.63580.19511440.16092634X-RAY DIFFRACTION100
5.6358-32.80120.1921980.21382694X-RAY DIFFRACTION100

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