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- PDB-8alk: Structure of the Legionella phosphocholine hydrolase Lem3 in comp... -

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Basic information

Entry
Database: PDB / ID: 8alk
TitleStructure of the Legionella phosphocholine hydrolase Lem3 in complex with its substrate Rab1
Components
  • Phosphocholine hydrolase Lem3
  • Ras-related protein Rab-1B
KeywordsHYDROLASE / Bacterial effector / dephosphocholinase / Legionella pneumophila
Function / homology
Function and homology information


phosphocholine hydrolase activity / positive regulation of glycoprotein metabolic process / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phagophore assembly site membrane / RAB geranylgeranylation / regulation of autophagosome assembly / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / regulation of GTPase activity ...phosphocholine hydrolase activity / positive regulation of glycoprotein metabolic process / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phagophore assembly site membrane / RAB geranylgeranylation / regulation of autophagosome assembly / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / regulation of GTPase activity / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / transport vesicle / COPI-mediated anterograde transport / endomembrane system / endoplasmic reticulum-Golgi intermediate compartment membrane / small monomeric GTPase / intracellular protein transport / G protein activity / host cell cytoplasm / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / extracellular region / cytosol
Similarity search - Function
: / PPM-type phosphatase-like domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases ...: / PPM-type phosphatase-like domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Chem-OJU / Phosphocholine hydrolase Lem3 / Ras-related protein Rab-1B
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKaspers, M.S. / Pett, C. / Hedberg, C. / 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
DepositionAug 1, 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 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphocholine hydrolase Lem3
B: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8388
Polymers72,6262
Non-polymers1,2126
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-71 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.332, 119.332, 79.058
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
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,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Phosphocholine hydrolase Lem3 / Dephosphocholinase Lem3


Mass: 52900.617 Da / Num. of mol.: 1 / Mutation: T391C, C395S, C134S, C209S, C456S
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: Protein Ras-related protein Rab-1B


Mass: 19725.363 Da / Num. of mol.: 1 / Mutation: S76T
Source method: isolated from a genetically manipulated source
Details: GDP is a non-covalently bound ligand and should not be reported as part of the polypeptide chain. The TPO residue is not an actual phospho-threonine but a threonine which is modified by a ...Details: GDP is a non-covalently bound ligand and should not be reported as part of the polypeptide chain. The TPO residue is not an actual phospho-threonine but a threonine which is modified by a phospho-choline analogue that cross-links the two proteins of the complex (see ligand section)
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1B / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q9H0U4, small monomeric GTPase

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Non-polymers , 4 types, 82 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-OJU / 2-[[[5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxyethyl-[3-(2-chloranylethanoylamino)propyl]-dimethyl-azanium / Cytidine-diphosphate with a thiol-reactive chloroacetamide (cross-linker)


Mass: 608.881 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H33ClN5O12P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / 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: 0.979124 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: 0.979124 Å / Relative weight: 1
ReflectionResolution: 2.15→103.34 Å / Num. obs: 34977 / % possible obs: 99.98 % / Redundancy: 13.6 % / Biso Wilson estimate: 44.63 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.124 / Net I/σ(I): 9.7
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2867 / CC1/2: 0.761 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Lem3_apo, 3NKV

3nkv


Resolution: 2.15→103.34 Å / SU ML: 0.228 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4627
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2275 1839 5.26 %
Rwork0.1813 33102 -
obs0.1837 34941 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.06 Å2
Refinement stepCycle: LAST / Resolution: 2.15→103.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4840 0 16 76 4932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274946
X-RAY DIFFRACTIONf_angle_d0.51916695
X-RAY DIFFRACTIONf_chiral_restr0.0446774
X-RAY DIFFRACTIONf_plane_restr0.0031848
X-RAY DIFFRACTIONf_dihedral_angle_d12.91813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.210.29851460.21972548X-RAY DIFFRACTION100
2.21-2.270.27581400.20782519X-RAY DIFFRACTION100
2.27-2.350.26341560.20412514X-RAY DIFFRACTION100
2.35-2.430.26771530.19882525X-RAY DIFFRACTION100
2.43-2.530.27981380.19252522X-RAY DIFFRACTION99.96
2.53-2.640.27171330.19442559X-RAY DIFFRACTION100
2.64-2.780.25321380.18872536X-RAY DIFFRACTION100
2.78-2.960.24351530.19242530X-RAY DIFFRACTION100
2.96-3.180.2671350.19862551X-RAY DIFFRACTION100
3.18-3.50.2322890.1912604X-RAY DIFFRACTION100
3.51-4.010.2171670.17112520X-RAY DIFFRACTION100
4.01-5.050.20931520.15562550X-RAY DIFFRACTION100
5.06-103.340.18881390.18212624X-RAY DIFFRACTION99.78
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)
13.62117651228-0.459708938366-1.110576924396.254438756553.65779522795.63388678614-0.05251803230620.2142832039220.208258063094-0.2738729646950.281660104628-0.405065392881-0.5228214138240.514275563831-0.3649145141680.368070882943-0.139626799281-0.04186009441320.2960221090780.03215670697770.345530823743-27.8704482396-4.234559950092.74690871189
22.40413434930.3109485800260.1214903750811.912488041011.672759171996.65437525815-0.1157779630420.2771701715270.0251932542996-0.3353610476080.147686980469-0.0830484352033-0.3686445821140.378693232729-0.06964067392040.311461984378-0.0189942213422-0.02633866950850.1996571227130.0142012732260.355103759065-29.0107588897-7.950470274777.65750221872
35.727338263990.746903351758-0.6205546179942.713846592151.324385991049.29215308923-0.3511510931170.190698796070.589671673627-0.3317366683440.1363270219690.281416206324-1.04632689396-0.608253451570.1842082995510.4904708576020.138240328627-0.1819490498720.329456386958-0.02553521049580.55924129693-43.4192787745-1.440970468788.63213169113
42.53687570626-0.1926882102031.557786994992.578759566851.543700725445.696670989240.240554135995-0.143313487993-0.2319167270320.126574657898-0.2410651485090.3056240828790.472708749011-0.674975250016-0.05151240604530.273973613507-0.0680607600979-0.005629946670020.3354685325450.02466548887190.386465043213-43.0001836245-17.820159072213.6769631363
51.357402215140.07744289375732.258248107221.252410657530.2634869187036.974112902030.2291706173630.0805723051073-0.5882728699170.2719607683020.180316718632-0.2410263927430.9241045814450.631116959339-0.3972090087060.4224627384860.120597185797-0.09649724226450.357998594476-0.04121152752470.458004125687-22.7162306977-19.995045466215.114280184
63.087367419760.9135417974291.013494327918.155156613017.004938525478.88509628413-0.1599991501070.43321941408-0.0721897422948-0.9251246319310.3065833243060.0750009825427-0.380891565070.272392848054-0.09378691584230.476010317468-0.0113030823081-0.03705947874290.539744806516-0.06614133511450.499952757941-27.7783231778-28.2620482997-17.1029380373
78.41976836694-1.58902084753-2.130661051694.383152347133.71800983176.88848905759-0.218412074265-0.205144980218-0.7136453777780.5736563254390.19478016641-0.1497567048621.126539855930.131173417770.007827634473090.6634172198410.0126696131326-0.1450915919660.305376350307-0.01421878678670.601578613199-35.9905713854-34.5383433934-13.1850166603
80.6468036173860.598452133911.320423486631.755248598652.638164574227.69841992089-0.0208617024915-0.032526504622-0.0246915398296-0.1100574687890.05913544950470.112262945183-0.357118571730.02375269644880.01376868452370.2936127764810.0493357433479-0.007396602717970.328326911395-0.01478010548160.406485976272-29.8298237775-8.9593409640423.5260761842
93.446878495510.3790495702442.634625584561.55823085580.9712274098082.32637188191-0.113365864711-0.1033928265090.1794756170720.08569564477950.0829395911916-0.152989851713-0.2392429513930.6273829251850.04258374866540.3646689891490.0260003843685-0.04486782326540.388618956361-0.08487466749840.393578428536-17.6832453078-5.4542150771730.1566768649
107.467089097023.511049269973.053034088448.029129926793.323043682584.96212357528-0.4507411319430.6192510159520.159510528849-0.3451444445210.556788799906-0.843349776671-0.4792766272270.697221203509-0.05480120530190.354439615974-0.0370482920559-0.06042678253070.6118153289880.02462838558850.548628442888-54.1728612466-9.75549875801-20.8632475881
117.21926600679-5.53832864340.008537178576124.30072573908-0.7445879589489.38805356763-0.310795822405-0.1139546959820.781518837282-0.453266670393-0.1513099378431.17515327928-0.80534643473-0.3878724163080.2227856698860.428776404307-0.0201100603312-0.129994654680.570593107108-0.04053593267550.703137349473-48.0061027133-20.30072081-7.14931907322
126.37303546997-0.3878540305883.610389608152.25209766691-0.01108303561767.507354042920.339402216304-0.344285848316-0.5250522752870.110061808719-0.0647694301629-0.07794838102270.582853726013-0.133631260832-0.2914183654830.317459174052-0.0269470328314-0.001199630075970.4232091281960.0120982523110.396498972692-66.0091108265-20.8600860016-16.3292438924
133.834393883590.633806362718-0.03131898708326.18297215653.964657858854.56333811795-0.03424153122480.1038905420290.386330203274-0.152677375197-0.288359248547-0.0609710422433-0.335000442659-0.3152233993760.3755104214880.3928981143340.107040612732-0.1389762999880.543501061730.03281404305440.484647471216-69.2240381205-11.9423568685-19.5735350388
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 20:37)AA20 - 371 - 18
22(chain A and resid 38:107)AA38 - 10719 - 88
33(chain A and resid 108:144)AA108 - 14489 - 123
44(chain A and resid 145:281)AA145 - 281124 - 245
55(chain A and resid 282:310)AA282 - 310246 - 274
66(chain A and resid 311:335)AA311 - 335275 - 299
77(chain A and resid 336:381)AA336 - 381300 - 345
88(chain A and resid 382:436)AA382 - 436346 - 400
99(chain A and resid 437:483)AA437 - 483401 - 447
1010(chain B and resid 2:67)BC2 - 671 - 58
1111(chain B and resid 68:80)BC68 - 8059 - 71
1212(chain B and resid 81:128)BC81 - 12872 - 118
1313(chain B and resid 129:173)BC129 - 173119 - 163

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