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- PDB-6cgk: Structure of the HAD domain of effector protein Lem4 (lpg1101) fr... -

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Basic information

Entry
Database: PDB / ID: 6cgk
TitleStructure of the HAD domain of effector protein Lem4 (lpg1101) from Legionella pneumophila (inactive mutant)with phosphate bound in the active site
Componentseffector protein Lem4 (lpg1101)
KeywordsHYDROLASE / haloacid dehalogenase superfamily / tyrosine phosphatase / translocated bacterial effector
Function / homology
Function and homology information


host cell cytoplasmic vesicle / small GTPase binding / metal ion binding
Similarity search - Function
DrrA phosphatidylinositol 4-phosphate binding domain / DrrA, PI4P binding domain superfamily / DrrA phosphatidylinositol 4-phosphate binding domain / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
PHOSPHATE ION / DrrA phosphatidylinositol 4-phosphate binding domain-containing protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.668 Å
AuthorsBeyrakhova, K.A. / Xu, C. / Cygler, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-48370 Canada
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Legionella pneumophilaeffector Lem4 is a membrane-associated protein tyrosine phosphatase.
Authors: Beyrakhova, K. / Li, L. / Xu, C. / Gagarinova, A. / Cygler, M.
History
DepositionFeb 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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: effector protein Lem4 (lpg1101)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9164
Polymers24,7051
Non-polymers2113
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.627, 105.627, 36.255
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein effector protein Lem4 (lpg1101)


Mass: 24704.826 Da / Num. of mol.: 1 / Mutation: D25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg1101 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL(DE3)pLysS / References: UniProt: Q5ZWI4
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris 6.5, 22% PEG 3350, 0.2 M Mg acetate, 0.6 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.668→52.814 Å / Num. obs: 24546 / % possible obs: 100 % / Redundancy: 14.3 % / Biso Wilson estimate: 22.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.024 / Rrim(I) all: 0.09 / Net I/σ(I): 19.7 / Num. measured all: 351125
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.668-1.67414.41.3592320.9150.3671.40897.1
7.734-52.81410.30.0392950.9990.0130.04295.2

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CGJ

6cgj


Resolution: 1.668→47.238 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.72
RfactorNum. reflection% reflection
Rfree0.2264 1199 4.9 %
Rwork0.1883 --
obs0.1901 24476 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.74 Å2 / Biso mean: 40.5311 Å2 / Biso min: 19.88 Å2
Refinement stepCycle: final / Resolution: 1.668→47.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 20 113 1684
Biso mean--57.93 43.42 -
Num. residues----196
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.668-1.73480.40381320.386425392671100
1.7348-1.81380.37361150.326925532668100
1.8138-1.90940.32921560.264825162672100
1.9094-2.0290.25271140.222625692683100
2.029-2.18570.27811360.203625422678100
2.1857-2.40560.22741290.170125842713100
2.4056-2.75370.21311300.172725872717100
2.7537-3.46920.21651530.180526122765100
3.4692-47.25680.17911340.15422775290999
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)
13.07661.49680.39873.54670.1650.62690.1739-0.1961-0.21480.1191-0.14510.20020.0702-0.037-0.03620.21720.00110.05670.24270.02620.293117.2147-0.03556.0588
23.84962.48681.12195.04341.16572.46220.1008-0.09620.4280.1524-0.12730.4476-0.1296-0.043-0.0120.2094-0.00530.07980.2170.04470.267921.45728.16166.7008
34.48681.33190.60143.06270.60281.42590.06720.1972-0.1749-0.00650.0387-0.1289-0.02730.2018-0.11580.2106-0.0020.02510.23720.01850.266531.64054.113.963
42.96632.7329-1.07682.9008-1.08465.49640.1016-0.8448-0.6970.76290.0708-0.73930.63960.1731-0.17010.42570.0321-0.09810.4765-0.00610.529739.38931.6212.9955
53.70740.66331.41026.948-0.98532.51910.2366-0.75630.09450.7633-0.22570.2085-0.20150.09820.12520.5602-0.12710.06140.5278-0.0090.305428.51289.921419.7331
62.9391-2.2087-4.56542.46953.9097.70670.63841.1644-0.2186-0.9733-0.3205-0.6559-1.1157-0.1836-0.47640.6505-0.07630.11780.6312-0.09090.689428.938725.598612.9105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 73 )A15 - 73
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 109 )A74 - 109
3X-RAY DIFFRACTION3chain 'A' and (resid 110 through 157 )A110 - 157
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 175 )A158 - 175
5X-RAY DIFFRACTION5chain 'A' and (resid 176 through 198 )A176 - 198
6X-RAY DIFFRACTION6chain 'A' and (resid 199 through 210 )A199 - 210

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