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- PDB-8agg: Structure of the Legionella phosphocholine hydrolase Lem3 -

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Basic information

Entry
Database: PDB / ID: 8agg
TitleStructure of the Legionella phosphocholine hydrolase Lem3
ComponentsPhosphocholine hydrolase Lem3
KeywordsHYDROLASE / Bacterial effector / dephosphocholinase / Legionella pneumophila
Function / homologyphosphocholine hydrolase activity / PPM-type phosphatase-like domain superfamily / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / regulation of GTPase activity / host cell cytoplasm / extracellular region / Phosphocholine hydrolase Lem3
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsKaspers, M.S. / Itzen, A. / Pogenberg, V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Dephosphocholination by Legionella effector Lem3 functions through remodelling of the switch II region of Rab1b.
Authors: Kaspers, M.S. / Pogenberg, V. / Pett, C. / Ernst, S. / Ecker, F. / Ochtrop, P. / Groll, M. / Hedberg, C. / Itzen, A.
History
DepositionJul 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphocholine hydrolase Lem3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0452
Polymers65,0211
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.022, 78.022, 382.014
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Phosphocholine hydrolase Lem3 / Dephosphocholinase Lem3


Mass: 65020.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lem3, lpg0696 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: Q5ZXN5, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
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: 2.6 Å3/Da / Density % sol: 52.65 % / Description: hexagonal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: MES 0.1M pH 5, PEG6000 5%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 3.6→67.57 Å / Num. obs: 8684 / % possible obs: 98.71 % / Redundancy: 24.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.1709 / Net I/σ(I): 14.2
Reflection shellResolution: 3.6→3.94 Å / Redundancy: 24.6 % / Rmerge(I) obs: 1.076 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2009 / CC1/2: 0.673 / % possible all: 99.7

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Processing

Software
NameVersionClassification
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASER2.8.3phasing
Coot0.9model building
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Lem3_apo

Resolution: 3.6→66.54 Å / SU ML: 0.5653 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.4503
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2988 409 4.71 %
Rwork0.2626 8266 -
obs0.2643 8675 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 171.29 Å2
Refinement stepCycle: LAST / Resolution: 3.6→66.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 1 0 3843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00143900
X-RAY DIFFRACTIONf_angle_d0.37645263
X-RAY DIFFRACTIONf_chiral_restr0.0378613
X-RAY DIFFRACTIONf_plane_restr0.0021676
X-RAY DIFFRACTIONf_dihedral_angle_d11.40551443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-4.120.3721300.29292669X-RAY DIFFRACTION99.26
4.12-5.190.35071450.26822697X-RAY DIFFRACTION99.09
5.19-66.540.25151340.25232900X-RAY DIFFRACTION97.9
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)
11.28775149814-0.880238754541.801244412593.9288091671-2.342874989884.0614873804-0.0643677719720.240760738173-0.329829886703-0.0002238822136290.294503704816-0.0299100041027-0.2221160621160.1143706548896.94730583746E-51.29482595671-0.01895070915890.08898580790471.475450990490.5001969330711.66537287175.29215333084-27.0372174407-1.73328433371
20.6840154320310.0591680273001-0.5473809750860.530194487602-0.2893084798370.489262135766-0.4002212987310.371623488393-0.9948354263240.151481787884-0.0873812078040.4275096215660.996620300425-0.444258127628-0.159166984161.979120021270.2027677957280.1331322142941.56080717780.904777378642.919522515286.20145507639-65.871583901925.3958380805
30.4623260191530.08515340958530.1517547821870.06537427239-0.1080387163170.173923902362-0.3344977217950.496470198063-0.989144078679-0.00725803035542-0.5951183165240.4145065241551.264795860290.15810739367-0.008170373536261.986138583620.146293535821-0.1068911164921.503887209520.5619504866942.357140521314.4127320608-70.361055727828.8404012125
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 468 )19 - 4681 - 416
22chain 'A' and (resid 469 through 508 )469 - 508417 - 449
33chain 'A' and (resid 509 through 565 )509 - 565450 - 489

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