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- PDB-6deh: Structure of LpnE Effector Protein from Legionella pneumophila (s... -

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Basic information

Entry
Database: PDB / ID: 6deh
TitleStructure of LpnE Effector Protein from Legionella pneumophila (sp. Philadelphia)
ComponentsTPR repeat protein, protein-protein interaction
KeywordsPROTEIN BINDING / SEL1-Like repeat (SLR) protein
Function / homology: / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / Tetratricopeptide-like helical domain superfamily / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / TPR repeat protein, protein-protein interaction
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVoth, K. / Chung, I.Y.W. / van Straaten, K.E. / Cygler, M.
CitationJournal: FEBS J. / Year: 2019
Title: The structure of Legionella effector protein LpnE provides insights into its interaction with Oculocerebrorenal syndrome of Lowe (OCRL) protein.
Authors: Voth, K.A. / Chung, I.Y.W. / van Straaten, K. / Li, L. / Boniecki, M.T. / Cygler, M.
History
DepositionMay 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: 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.year / _citation_author.name
Revision 1.2Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TPR repeat protein, protein-protein interaction
B: TPR repeat protein, protein-protein interaction
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8108
Polymers72,3432
Non-polymers4666
Water5,567309
1
A: TPR repeat protein, protein-protein interaction
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, PISA indicates significant dimer interface is contributed by the hexa-histidine tag and connecting residues. This dimer disappears when the tag is removed (as evidenced by gel filtration).
  • 36.6 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)36,5796
Polymers36,1721
Non-polymers4085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TPR repeat protein, protein-protein interaction
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2302
Polymers36,1721
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.704, 84.064, 128.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TPR repeat protein, protein-protein interaction


Mass: 36171.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2222 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZTE0
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 0.2 M ammonium sulfate, 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→48.77 Å / Num. obs: 74365 / % possible obs: 99.83 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.072 / Net I/σ(I): 21.12
Reflection shellResolution: 1.8→1.864 Å / Mean I/σ(I) obs: 1.81 / Num. unique obs: 11787 / CC1/2: 0.724 / Rrim(I) all: 1.387

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OUV

1ouv


Resolution: 1.8→48.77 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.4
RfactorNum. reflection% reflection
Rfree0.214 1845 2.69 %
Rwork0.1891 --
obs0.1898 68564 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5011 0 22 309 5342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115171
X-RAY DIFFRACTIONf_angle_d1.0716993
X-RAY DIFFRACTIONf_dihedral_angle_d13.6562983
X-RAY DIFFRACTIONf_chiral_restr0.062688
X-RAY DIFFRACTIONf_plane_restr0.007930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84870.3111410.26985067X-RAY DIFFRACTION100
1.8487-1.90310.26841400.23675073X-RAY DIFFRACTION100
1.9031-1.96450.25581410.21195082X-RAY DIFFRACTION100
1.9645-2.03470.2191390.19975065X-RAY DIFFRACTION100
2.0347-2.11620.24271410.19955090X-RAY DIFFRACTION100
2.1162-2.21250.22631410.18735078X-RAY DIFFRACTION100
2.2125-2.32910.23411410.18995102X-RAY DIFFRACTION100
2.3291-2.47510.27911410.20235095X-RAY DIFFRACTION100
2.4751-2.66620.25991410.20655114X-RAY DIFFRACTION100
2.6662-2.93440.24431420.20595162X-RAY DIFFRACTION100
2.9344-3.3590.2221430.20255167X-RAY DIFFRACTION100
3.359-4.23160.18931450.16945214X-RAY DIFFRACTION100
4.2316-48.78880.16171490.16695410X-RAY DIFFRACTION100

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