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- PDB-7ew8: Legionella pneumophila effector AnkD -

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Basic information

Entry
Database: PDB / ID: 7ew8
TitleLegionella pneumophila effector AnkD
ComponentsANK_REP_REGION domain-containing protein
KeywordsTOXIN / Legionella pneumophila effector / Lipid droplet / vesicle trafficking
Function / homologyAnkyrin repeat profile. / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.594 Å
AuthorsChen, T.T. / Lin, Y.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2022
Title: Atypical Legionella GTPase effector hijacks host vesicular transport factor p115 to regulate host lipid droplet.
Authors: Chen, T.T. / Lin, Y. / Zhang, S. / Liu, S. / Song, L. / Zhong, W. / Luo, Z.Q. / Han, A.
History
DepositionMay 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 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: ANK_REP_REGION domain-containing protein
B: ANK_REP_REGION domain-containing protein


Theoretical massNumber of molelcules
Total (without water)110,3272
Polymers110,3272
Non-polymers00
Water2,702150
1
A: ANK_REP_REGION domain-containing protein


Theoretical massNumber of molelcules
Total (without water)55,1641
Polymers55,1641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ANK_REP_REGION domain-containing protein


Theoretical massNumber of molelcules
Total (without water)55,1641
Polymers55,1641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.058, 75.997, 104.814
Angle α, β, γ (deg.)90.000, 90.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ANK_REP_REGION domain-containing protein / AnkD


Mass: 55163.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_12350, DI026_04400 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F2G5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: magnesium chloride, Bis Tris, PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 32269 / % possible obs: 92.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 21
Reflection shellResolution: 2.59→2.63 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 15131 / CC1/2: 0.843 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.594→45.207 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2679 1485 4.95 %
Rwork0.201 28529 -
obs0.2043 32269 92.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.1 Å2 / Biso mean: 49.8776 Å2 / Biso min: 11.44 Å2
Refinement stepCycle: final / Resolution: 2.594→45.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6676 0 0 150 6826
Biso mean---38.29 -
Num. residues----860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096854
X-RAY DIFFRACTIONf_angle_d1.1169212
X-RAY DIFFRACTIONf_chiral_restr0.052996
X-RAY DIFFRACTIONf_plane_restr0.0081218
X-RAY DIFFRACTIONf_dihedral_angle_d3.6284256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5942-2.6780.3595660.2413178664
2.678-2.77370.28661170.2239210076
2.7737-2.88470.28131660.2385236186
2.8847-3.0160.29981270.238265795
3.016-3.17490.35121260.2499277799
3.1749-3.37380.27671400.21672781100
3.3738-3.63420.30261640.21492767100
3.6342-3.99970.27551330.18842816100
3.9997-4.5780.25251470.1732793100
4.578-5.76590.23231710.18412793100
5.7659-45.2070.22111280.17962898100

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