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

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Basic information

Entry
Database: PDB / ID: 6yhv
TitleStructural insights into Pseudomonas aeruginosa Type six secretion system exported effector 8: unliganded Tse8
ComponentsTse8
KeywordsTOXIN / Amidase Signature (AS) superfamily complex
Function / homologyAmidase signature domain / Amidase signature (AS) superfamily / Amidase / metal ion binding / COPPER (II) ION / Amidase domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.893 Å
AuthorsSainz-Polo, M.A. / Capuni, R. / Pretre, G. / Gonzalez-Magana, A. / Lucas, M. / Altuna, J. / Montanchez, I. / Fucini, P. / 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
DepositionMar 31, 2020Deposition 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

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Assembly

Deposited unit
A: Tse8
B: Tse8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,0983
Polymers127,0352
Non-polymers641
Water11,205622
1
A: Tse8


Theoretical massNumber of molelcules
Total (without water)63,5171
Polymers63,5171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tse8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5812
Polymers63,5171
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.506, 68.078, 77.604
Angle α, β, γ (deg.)72.94, 68.84, 79.27
Int Tables number1
Space group name H-MP1

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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 / Gene: PA4163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HWL8
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium acetate, 0.1 M Sodium cacodylate pH 6.5 and 18% PEG8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.893→42.83 Å / Num. obs: 94264 / % possible obs: 93.55 % / Redundancy: 3.5 % / CC1/2: 0.953 / CC star: 0.988 / Net I/σ(I): 5.22
Reflection shellResolution: 1.893→1.96 Å / Rmerge(I) obs: 1.459 / Num. unique obs: 8315

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TE4

6te4


Resolution: 1.893→42.83 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.93 / Phase error: 27.41
RfactorNum. reflection% reflection
Rfree0.2254 1997 2.22 %
Rwork0.1864 --
obs0.1873 90077 93.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.893→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8439 0 1 622 9062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048646
X-RAY DIFFRACTIONf_angle_d0.57311809
X-RAY DIFFRACTIONf_dihedral_angle_d9.665191
X-RAY DIFFRACTIONf_chiral_restr0.0431307
X-RAY DIFFRACTIONf_plane_restr0.0051591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.893-1.94040.37161250.3565601X-RAY DIFFRACTION84
1.9404-1.99280.32131490.32716312X-RAY DIFFRACTION93
1.9928-2.05150.32361330.30856224X-RAY DIFFRACTION93
2.0515-2.11770.3211430.29146213X-RAY DIFFRACTION92
2.1177-2.19340.28061420.2546237X-RAY DIFFRACTION93
2.1934-2.28120.29731460.22376320X-RAY DIFFRACTION94
2.2812-2.3850.27611370.20616392X-RAY DIFFRACTION95
2.385-2.51070.22611520.19256462X-RAY DIFFRACTION96
2.5107-2.6680.23311480.18256421X-RAY DIFFRACTION96
2.668-2.8740.25651370.19076453X-RAY DIFFRACTION96
2.874-3.16310.23571540.18196392X-RAY DIFFRACTION95
3.1631-3.62060.20241400.16566371X-RAY DIFFRACTION95
3.6206-4.56070.16151490.13516382X-RAY DIFFRACTION95

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