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- PDB-6te4: Structural insights into Pseudomonas aeruginosa Type six secretio... -

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Basic information

Entry
Database: PDB / ID: 6te4
TitleStructural insights into Pseudomonas aeruginosa Type six secretion system exported effector 8: Tse8 in complex with a peptide
Components
  • Pro-Pro-Leu-Ala-Ser-Lys
  • Tse8
KeywordsTOXIN / Amidase Signature (AS) superfamily complex
Function / homologyAmidase signature domain / Amidase signature (AS) superfamily / Amidase / metal ion binding / Amidase domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Escherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsSainz-Polo, M.A. / Capuni, R. / Lucas, M. / Altuna, J. / Fucini, P. / Montanchez, I. / Albesa-Jove, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesCTQ2016-76941-R Spain
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structural insights into Pseudomonas aeruginosaType six secretion system exported effector 8.
Authors: Gonzalez-Magana, A. / Sainz-Polo, M.A. / Pretre, G. / Capuni, R. / Lucas, M. / Altuna, J. / Montanchez, I. / Fucini, P. / Albesa-Jove, D.
History
DepositionNov 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tse8
B: Tse8
C: Pro-Pro-Leu-Ala-Ser-Lys


Theoretical massNumber of molelcules
Total (without water)127,6473
Polymers127,6473
Non-polymers00
Water9,008500
1
A: Tse8
C: Pro-Pro-Leu-Ala-Ser-Lys


Theoretical massNumber of molelcules
Total (without water)64,1302
Polymers64,1302
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-9 kcal/mol
Surface area18960 Å2
MethodPISA
2
B: Tse8


Theoretical massNumber of molelcules
Total (without water)63,5171
Polymers63,5171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.440, 73.611, 77.668
Angle α, β, γ (deg.)97.970, 114.950, 104.510
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Tse8


Mass: 63517.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA4163 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HWL8
#2: Protein/peptide Pro-Pro-Leu-Ala-Ser-Lys


Mass: 612.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: peptide that might be cleaved from the C-terminal part of the protein as identified by MS analysis.
Source: (natural) Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.66 Å3/Da / Density % sol: 53.71 % / Description: prisms
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M magnesium sulfate heptahydrate, 0.1 M MES buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.29→56.632 Å / Num. obs: 53333 / % possible obs: 94.85 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.48 Å2 / CC1/2: 0.979 / CC star: 0.995 / Rmerge(I) obs: 0.1873 / Rpim(I) all: 0.1199 / Rrim(I) all: 0.2233 / Net I/σ(I): 6.96
Reflection shellResolution: 2.29→2.32 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.7321 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 2646 / CC1/2: 0.852 / CC star: 0.959 / R split: 0.4686 / Rrim(I) all: 0.8725 / % possible all: 90.26

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1m22

1m22


Resolution: 2.29→56.632 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.02
RfactorNum. reflection% reflectionSelection details
Rfree0.2725 1980 3.74 %random selection
Rwork0.2461 ---
obs0.2471 52983 94.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.97 Å2 / Biso mean: 24.63 Å2 / Biso min: 12.3 Å2
Refinement stepCycle: final / Resolution: 2.29→56.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8398 0 0 500 8898
Biso mean---27.57 -
Num. residues----1135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038601
X-RAY DIFFRACTIONf_angle_d0.53311759
X-RAY DIFFRACTIONf_chiral_restr0.0441308
X-RAY DIFFRACTIONf_plane_restr0.0061579
X-RAY DIFFRACTIONf_dihedral_angle_d14.5023105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.29-2.34710.3452990.2948340188
2.3471-2.41060.32911980.2885363296
2.4106-2.48150.3129990.2969371696
2.4815-2.56160.29731980.2826364196
2.5616-2.65320.297990.2683374396
2.6532-2.75940.31541980.2688362496
2.7594-2.8850.3212990.2693372596
2.885-3.0370.3273990.2685373996
3.037-3.22730.27461980.2513362796
3.2273-3.47650.2761990.2344375496
3.4765-3.82620.26781980.2695343291
3.8262-4.37970.242990.1986368095
4.3797-5.51730.20371980.1967358195
5.5173-56.6320.2085990.2169370895

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