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- PDB-5n6x: Crystal structure of the Legionella effector WipA -

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Basic information

Entry
Database: PDB / ID: 5n6x
TitleCrystal structure of the Legionella effector WipA
ComponentsWipA
KeywordsHYDROLASE / Legionella effector / tyrosine phosphatase / phosphoesterase fold / coiled-coil
Function / homology
Function and homology information


phosphatase activity / metal ion binding
Similarity search - Function
: / WipA, alpha-helical hairpin / : / WipA-like, phosphatase domain / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / BROMIDE ION / : / PHOSPHATE ION / WipA
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 16, 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 1, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WipA
B: WipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,53917
Polymers96,3362
Non-polymers1,20415
Water11,331629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-73 kcal/mol
Surface area35310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.650, 80.650, 321.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein WipA


Mass: 48167.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: wipA / Production host: Escherichia coli (E. coli) / References: UniProt: Q5GA16

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Non-polymers , 6 types, 644 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 629 / 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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris Propane pH7.5, 0.2 M NaBr and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.75→46.533 Å / Num. obs: 108230 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rrim(I) all: 0.077 / Net I/σ(I): 13.94
Reflection shellResolution: 1.75→1.84 Å / Mean I/σ(I) obs: 1.25 / CC1/2: 0.555 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WipA411

Resolution: 1.75→46.533 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 2559 2.36 %
Rwork0.1798 --
obs0.1807 108219 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→46.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6521 0 40 629 7190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076805
X-RAY DIFFRACTIONf_angle_d0.8449215
X-RAY DIFFRACTIONf_dihedral_angle_d17.234119
X-RAY DIFFRACTIONf_chiral_restr0.0541020
X-RAY DIFFRACTIONf_plane_restr0.0051185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78370.37271150.33475804X-RAY DIFFRACTION100
1.7837-1.82010.37851130.31175754X-RAY DIFFRACTION100
1.8201-1.85970.32591180.27275803X-RAY DIFFRACTION100
1.8597-1.90290.29711160.26215830X-RAY DIFFRACTION100
1.9029-1.95050.28751230.25475778X-RAY DIFFRACTION100
1.9505-2.00330.26641310.22495831X-RAY DIFFRACTION100
2.0033-2.06220.24631410.21265786X-RAY DIFFRACTION100
2.0622-2.12880.20681100.19475850X-RAY DIFFRACTION100
2.1288-2.20490.22621610.18775788X-RAY DIFFRACTION100
2.2049-2.29310.24171700.18745820X-RAY DIFFRACTION100
2.2931-2.39750.21021560.17785798X-RAY DIFFRACTION100
2.3975-2.52390.21041610.17575856X-RAY DIFFRACTION100
2.5239-2.6820.21051690.18135838X-RAY DIFFRACTION100
2.682-2.88910.23271670.18815866X-RAY DIFFRACTION100
2.8891-3.17970.22491530.18215908X-RAY DIFFRACTION100
3.1797-3.63970.21841600.16735954X-RAY DIFFRACTION100
3.6397-4.5850.19021440.14696030X-RAY DIFFRACTION100
4.585-46.54980.17791510.16536366X-RAY DIFFRACTION99
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)
11.2872-2.20430.9263.5588-1.47690.8469-0.0630.07560.25340.1224-0.1139-0.3755-0.04440.09020.16910.244-0.0625-0.01120.38240.02890.3225-2.4189-21.7229-22.1644
22.1699-0.24250.26161.749-0.22331.73460.05060.18120.0945-0.1563-0.0641-0.0112-0.00230.04890.02580.2289-0.02970.01690.26720.00380.2099-2.2459-39.1046-24.0112
32.62510.5310.13892.6274-0.13522.18310.1305-0.239-0.27180.2828-0.10930.10440.1217-0.1242-0.01570.2372-0.09090.01360.23990.02180.2261-15.5838-54.0986-14.61
41.206-1.34510.13783.92210.78480.99610.17920.2227-0.22820.0497-0.23350.27580.1904-0.33420.23010.3161-0.1382-0.0260.44370.02130.36-48.922-22.7289-24.4827
51.54790.38670.14571.79190.943.0891-0.01160.1654-0.068-0.10380.01120.0444-0.0112-0.23240.01090.2229-0.0434-0.02810.32180.03310.2601-48.4494-5.5255-25.4479
61.5890.1732-0.26351.8122-0.19843.59430.0133-0.01380.08550.17530.0076-0.0515-0.37720.1419-0.07010.2489-0.0797-0.04030.24430.0230.2093-35.68067.7578-13.0401
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 23:171))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 172:273))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 274:418))
4X-RAY DIFFRACTION4chain 'B' and ((resseq 23:171))
5X-RAY DIFFRACTION5chain 'B' and ((resseq 172:273))
6X-RAY DIFFRACTION6chain 'B' and ((resseq 274:422))

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