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- PDB-5n72: Crystal structure of the Legionella effector WipA shorter construct -

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Basic information

Entry
Database: PDB / ID: 5n72
TitleCrystal structure of the Legionella effector WipA shorter construct
ComponentsWipA
KeywordsHYDROLASE / Legionella effector / tyrosine phosphatase / phosphoesterase fold / coiled-coil
Function / homology: / WipA, alpha-helical hairpin / : / WipA-like, phosphatase domain / Metallo-dependent phosphatase-like / phosphatase activity / metal ion binding / ACETATE ION / WipA
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.842 Å
AuthorsPinotsis, N. / Waksman, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council321630 United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structure of the WipA protein reveals a novel tyrosine protein phosphatase effector from Legionella pneumophila.
Authors: Pinotsis, N. / Waksman, G.
History
DepositionFeb 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4355
Polymers47,1991
Non-polymers2364
Water2,774154
1
A: WipA
hetero molecules

A: WipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,87010
Polymers94,3972
Non-polymers4728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3620 Å2
ΔGint-14 kcal/mol
Surface area36280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.060, 57.480, 80.710
Angle α, β, γ (deg.)90.00, 91.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-608-

HOH

21A-704-

HOH

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Components

#1: Protein WipA


Mass: 47198.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: From 1-25 from vector / Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: wipA / Production host: Escherichia coli (E. coli) / References: UniProt: Q5GA16
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium acetate and 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.84→80.69 Å / Num. obs: 38861 / % possible obs: 94.5 % / Redundancy: 3.3 % / Rpim(I) all: 0.039 / Net I/σ(I): 16.2
Reflection shellResolution: 1.84→1.94 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.58

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.842→43.034 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 2056 5.43 %
Rwork0.2189 --
obs0.2211 37834 92.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.842→43.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 16 154 3333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053302
X-RAY DIFFRACTIONf_angle_d0.6844471
X-RAY DIFFRACTIONf_dihedral_angle_d18.4341997
X-RAY DIFFRACTIONf_chiral_restr0.046496
X-RAY DIFFRACTIONf_plane_restr0.004582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8422-1.8850.67361310.69242336X-RAY DIFFRACTION93
1.885-1.93220.7453420.638929X-RAY DIFFRACTION44
1.9322-1.98440.39871320.39552473X-RAY DIFFRACTION98
1.9844-2.04280.35331450.3152516X-RAY DIFFRACTION99
2.0428-2.10870.3291320.29682585X-RAY DIFFRACTION99
2.1087-2.18410.31141440.28882540X-RAY DIFFRACTION99
2.1841-2.27160.46851100.41112084X-RAY DIFFRACTION81
2.2716-2.37490.30481350.27642530X-RAY DIFFRACTION98
2.3749-2.50010.31511440.25962553X-RAY DIFFRACTION99
2.5001-2.65670.31991470.25822547X-RAY DIFFRACTION99
2.6567-2.86180.28961330.24392553X-RAY DIFFRACTION99
2.8618-3.14980.30112030.23752477X-RAY DIFFRACTION98
3.1498-3.60530.22011250.20922561X-RAY DIFFRACTION98
3.6053-4.54150.21151860.16982517X-RAY DIFFRACTION98
4.5415-43.04560.19951470.16282577X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7062-0.32121.42180.4333-0.50181.33620.1146-0.3643-0.00010.05940.05370.1024-0.0761-0.2525-00.4096-0.01620.03310.44120.00030.418225.438551.864439.701
23.41310.5064-2.41012.03140.09913.3977-0.1018-0.6886-0.16440.3223-0.0212-0.08620.19940.7657-0.01270.45380.0754-0.01390.44070.04310.389526.788849.64622.6247
32.4983-0.17030.75874.4907-1.22543.07290.0522-0.28750.15410.1423-0.1736-0.0755-0.2960.7362-0.00010.3256-0.00810.03090.4976-0.00810.321940.638762.43477.9238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 24:171))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 172:273))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 274:410))

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