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- PDB-6mca: Structure of Legionella Effector AnkH -

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Basic information

Entry
Database: PDB / ID: 6mca
TitleStructure of Legionella Effector AnkH
ComponentsAnkyrin repeat domain protein
KeywordsCELL INVASION / LegA3 / AnkH / cysteine protease-like / bacterial effector
Function / homology: / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / L(+)-TARTARIC ACID / Ankyrin repeat domain protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.455 Å
AuthorsCygler, M. / Chung, I.Y.W.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 48370 Canada
CitationJournal: Mbio / Year: 2019
Title: Interaction of the Ankyrin H Core Effector ofLegionellawith the Host LARP7 Component of the 7SK snRNP Complex.
Authors: Von Dwingelo, J. / Chung, I.Y.W. / Price, C.T. / Li, L. / Jones, S. / Cygler, M. / Abu Kwaik, Y.
History
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ankyrin repeat domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8576
Polymers56,2811
Non-polymers5765
Water5,603311
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint1 kcal/mol
Surface area20980 Å2
Unit cell
Length a, b, c (Å)102.125, 102.125, 265.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-902-

HOH

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Components

#1: Protein Ankyrin repeat domain protein / AnkH


Mass: 56281.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: legA3, lpg2300 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZT65
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 3.56 Å3/Da / Density % sol: 65.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.0 M ammonium tartrate dibasic, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 14, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.45→51.1 Å / Num. obs: 30920 / % possible obs: 97.3 % / Redundancy: 20.8 % / Biso Wilson estimate: 32.4 Å2 / Rrim(I) all: 0.082 / Net I/σ(I): 48.1
Reflection shellResolution: 2.45→2.49 Å / Mean I/σ(I) obs: 6.1 / Rrim(I) all: 0.855

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.455→51.063 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.39
RfactorNum. reflection% reflection
Rfree0.2237 1509 5.02 %
Rwork0.1844 --
obs0.1864 30064 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.455→51.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 38 311 4063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023872
X-RAY DIFFRACTIONf_angle_d0.4755252
X-RAY DIFFRACTIONf_dihedral_angle_d8.7373181
X-RAY DIFFRACTIONf_chiral_restr0.038576
X-RAY DIFFRACTIONf_plane_restr0.004680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4547-2.53390.32471000.24681944X-RAY DIFFRACTION75
2.5339-2.62450.30121340.24792507X-RAY DIFFRACTION96
2.6245-2.72950.28221680.21732572X-RAY DIFFRACTION100
2.7295-2.85370.24561230.21742649X-RAY DIFFRACTION100
2.8537-3.00420.2361440.2132612X-RAY DIFFRACTION100
3.0042-3.19240.28091460.21022623X-RAY DIFFRACTION100
3.1924-3.43880.26681350.20052640X-RAY DIFFRACTION100
3.4388-3.78480.22291440.18012663X-RAY DIFFRACTION100
3.7848-4.33220.18751310.1472689X-RAY DIFFRACTION100
4.3322-5.45710.1851280.14622751X-RAY DIFFRACTION100
5.4571-51.07350.1751560.17792905X-RAY DIFFRACTION99

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