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- PDB-8anp: Legionella effector Lem3 mutant D190A in complex with Mg2+ -

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Basic information

Entry
Database: PDB / ID: 8anp
TitleLegionella effector Lem3 mutant D190A in complex with Mg2+
ComponentsPhosphocholine hydrolase Lem3
KeywordsMETAL BINDING PROTEIN / Legionella effector Lem3 displaces the switch II region of Rab1b for dephosphocholination
Function / homologyphosphocholine hydrolase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / PPM-type phosphatase-like domain superfamily / regulation of GTPase activity / host cell cytoplasm / extracellular region / TRIETHYLENE GLYCOL / Phosphocholine hydrolase Lem3
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKaspers, M.S. / Pogenberg, V. / Ernst, S. / Ecker, F. / Pett, C. / Ochtrop, P. / Hedberg, C. / Groll, M. / Itzen, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1335 Germany
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 5, 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.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 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

Downloads & links

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Assembly

Deposited unit
A: Phosphocholine hydrolase Lem3
B: Phosphocholine hydrolase Lem3
C: Phosphocholine hydrolase Lem3
D: Phosphocholine hydrolase Lem3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,11615
Polymers212,3994
Non-polymers71711
Water4,864270
1
A: Phosphocholine hydrolase Lem3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2994
Polymers53,1001
Non-polymers1993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphocholine hydrolase Lem3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3955
Polymers53,1001
Non-polymers2954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phosphocholine hydrolase Lem3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2994
Polymers53,1001
Non-polymers1993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phosphocholine hydrolase Lem3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1242
Polymers53,1001
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.720, 187.690, 193.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Phosphocholine hydrolase Lem3 / Dephosphocholinase Lem3


Mass: 53099.828 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lem3, lpg0696 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5ZXN5, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES; 30% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 103694 / % possible obs: 99.8 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.5
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 12784

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Lem3 determined by SAD (thiomersal derivate)

Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.742 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 5165 5 %RANDOM
Rwork0.19 ---
obs0.1921 98136 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.57 Å2 / Biso mean: 51.987 Å2 / Biso min: 26.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å2-0 Å2-0 Å2
2--1.13 Å2-0 Å2
3----2.11 Å2
Refinement stepCycle: final / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13501 0 42 271 13814
Biso mean--61.63 47.13 -
Num. residues----1704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01313767
X-RAY DIFFRACTIONr_bond_other_d0.0010.01513117
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.64218582
X-RAY DIFFRACTIONr_angle_other_deg1.0781.5830255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46851689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55122.912728
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.973152408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4691580
X-RAY DIFFRACTIONr_chiral_restr0.0380.21916
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215407
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023065
X-RAY DIFFRACTIONr_rigid_bond_restr0.44326884
LS refinement shellResolution: 2.2→2.256 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 371 -
Rwork0.223 7050 -
all-7421 -
obs--99.96 %
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)
12.05850.80861.3811.9921.35432.9647-0.03280.04710.0794-0.01390.0230.0022-0.0203-0.0760.00980.03130.00250.07540.00890.01090.2061-1.9574-64.341638.5872
22.32990.3784-0.8081.643-0.56121.4351-0.12610.2255-0.0269-0.15090.0641-0.16560.0810.02570.0620.0393-0-0.03610.0436-0.03790.136-25.3171-29.874140.2315
32.2449-1.741-1.11663.82971.38771.7095-0.1728-0.0199-0.17680.42450.0286-0.08040.2430.10660.14430.1037-0.042-0.00090.08760.03580.0861-12.7666-8.819979.8367
42.7975-2.48121.5934.7295-1.54992.3522-0.16510.01590.22410.38430.0314-0.1454-0.146-0.07940.13370.1343-0.0408-0.04630.1154-0.00630.1177-15.338-88.166676.8872
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 601
2X-RAY DIFFRACTION2B20 - 602
3X-RAY DIFFRACTION3C19 - 601
4X-RAY DIFFRACTION4D19 - 501

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