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

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Basic information

Entry
Database: PDB / ID: 6cgj
TitleStructure of the HAD domain of effector protein Lem4 (lpg1101) from Legionella pneumophila
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
ACETATE ION / DrrA phosphatidylinositol 4-phosphate binding domain-containing protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 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 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)24,8814
Polymers24,7061
Non-polymers1753
Water3,027168
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)105.830, 105.830, 31.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-535-

HOH

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Components

#1: Protein effector protein Lem4 (lpg1101)


Mass: 24705.812 Da / Num. of mol.: 1
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): BL21(DE3)pLysS / References: UniProt: Q5ZWI4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 168 / 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: 1.8 Å3/Da / Density % sol: 31.48 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES 6.5, 0.2 M Magnesium acetate, 18% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9801 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.75→47.329 Å / Num. obs: 18738 / % possible obs: 99.7 % / Redundancy: 13.505 % / Biso Wilson estimate: 17.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.07 / Χ2: 0.995 / Net I/σ(I): 25.28 / Num. measured all: 253049 / Scaling rejects: 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.89.7840.3615.7413060.9740.3896.7
1.8-1.8412.0510.2868.2413410.9870.299100
1.84-1.914.1750.25110.5312790.9910.26100
1.9-1.9614.3170.19113.3112480.9950.198100
1.96-2.0214.3080.15815.7912170.9950.163100
2.02-2.0914.20.14717.1312030.9960.152100
2.09-2.1714.310.11221.0811150.9980.116100
2.17-2.2614.10.10223.1111200.9980.10699.9
2.26-2.3614.2220.08626.5810360.9980.08999.9
2.36-2.4713.9190.08427.9610220.9990.087100
2.47-2.6114.020.07830.469650.9980.081100
2.61-2.7713.9120.06933.289140.9980.071100
2.77-2.9613.8020.06136.818740.9990.063100
2.96-3.213.7230.05639.718260.9990.058100
3.2-3.513.5840.05244.257450.9990.054100
3.5-3.9113.6240.04447.36870.9990.04699.9
3.91-4.5213.4940.04449.536220.9990.045100
4.52-5.5313.2990.04449.715250.9990.045100
5.53-7.8312.7620.04347.14290.9990.045100
7.83-47.32911.1250.04546.892640.9980.04799.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→47.329 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.1
RfactorNum. reflection% reflection
Rfree0.1979 937 5 %
Rwork0.158 --
obs0.16 18733 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.85 Å2 / Biso mean: 24.7024 Å2 / Biso min: 9.32 Å2
Refinement stepCycle: final / Resolution: 1.75→47.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 11 168 1687
Biso mean--56.06 32.56 -
Num. residues----192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.84230.22951290.17012447257698
1.8423-1.95770.2311310.160724982629100
1.9577-2.10890.20921320.158225102642100
2.1089-2.32110.18011320.158625102642100
2.3211-2.6570.21291340.165425362670100
2.657-3.34740.23311350.170325672702100
3.3474-47.34590.16561440.145527282872100
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)
15.12561.39160.15133.62390.63752.5140.1711-0.2837-0.12380.2003-0.19160.06790.0881-0.05460.00750.07810.03-0.01890.1053-0.01320.071627.27834.03698.9198
23.6090.62311.08842.34470.53931.46340.0538-0.1530.01660.0746-0.06210.1850.0089-0.11360.00550.09930.00090.02080.11450.00050.101716.64453.53424.8732
33.35760.76270.45152.40890.61861.99010.0462-0.0124-0.05150.03620.0641-0.10910.01680.1282-0.11130.09760.00270.00710.12050.00560.122535.18043.89116.4625
44.7881.6236-0.0688.1368-0.13283.29450.0888-0.25890.40920.5143-0.0226-0.2306-0.3880.1229-0.06230.232-0.0040.00750.2545-0.06210.141228.357913.814417.9359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 39 )A15 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 112 )A40 - 112
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 182 )A113 - 182
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 206 )A183 - 206

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