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- PDB-7kj6: Structure of Legionella Effector LegA15 -

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Basic information

Entry
Database: PDB / ID: 7kj6
TitleStructure of Legionella Effector LegA15
ComponentsAnkyrin repeat-containing protein
KeywordsCELL INVASION / Bacterial effector
Function / homology: / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / DI(HYDROXYETHYL)ETHER / Ankyrin repeat-containing protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsCygler, M. / Chung, I.Y.W.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Legionella effector LegA15/AnkH contains an unrecognized cysteine protease-like domain and displays structural similarity to LegA3/AnkD, but differs in host cell localization.
Authors: Chung, I.Y.W. / Li, L. / Cygler, M.
History
DepositionOct 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 1.2Oct 9, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ankyrin repeat-containing protein
B: Ankyrin repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,25311
Polymers105,4072
Non-polymers8469
Water4,576254
1
A: Ankyrin repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1956
Polymers52,7031
Non-polymers4925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ankyrin repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0575
Polymers52,7031
Non-polymers3544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.160, 75.050, 108.530
Angle α, β, γ (deg.)90.000, 99.462, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLEULEU(chain 'A' and (resid 19 or (resid 20 and (name...AA19 - 2421 - 26
12LEULEULYSLYS(chain 'A' and (resid 19 or (resid 20 and (name...AA27 - 2829 - 30
13ASNASNSERSER(chain 'A' and (resid 19 or (resid 20 and (name...AA31 - 3333 - 35
14GLUGLULYSLYS(chain 'A' and (resid 19 or (resid 20 and (name...AA36 - 4538 - 47
15SERSERLEULEU(chain 'A' and (resid 19 or (resid 20 and (name...AA48 - 5450 - 56
16LYSLYSLYSLYS(chain 'A' and (resid 19 or (resid 20 and (name...AA5658
17ASPASPASNASN(chain 'A' and (resid 19 or (resid 20 and (name...AA60 - 6162 - 63
18PHEPHEGLUGLU(chain 'A' and (resid 19 or (resid 20 and (name...AA64 - 7066 - 72
19SERSERALAALA(chain 'A' and (resid 19 or (resid 20 and (name...AA73 - 11675 - 118
110LYSLYSVALVAL(chain 'A' and (resid 19 or (resid 20 and (name...AA119 - 142121 - 144
111ILEILEGLNGLN(chain 'A' and (resid 19 or (resid 20 and (name...AA145 - 199147 - 201
112THRTHRARGARG(chain 'A' and (resid 19 or (resid 20 and (name...AA202 - 241204 - 243
113PROPROHISHIS(chain 'A' and (resid 19 or (resid 20 and (name...AA243 - 268245 - 270
114GLYGLYTHRTHR(chain 'A' and (resid 19 or (resid 20 and (name...AA271 - 289273 - 291
115GLYGLYASNASN(chain 'A' and (resid 19 or (resid 20 and (name...AA292 - 319294 - 321
116THRTHRGLUGLU(chain 'A' and (resid 19 or (resid 20 and (name...AA322 - 333324 - 335
117SERSERSERSER(chain 'A' and (resid 19 or (resid 20 and (name...AA336 - 391338 - 393
118ASPASPLYSLYS(chain 'A' and (resid 19 or (resid 20 and (name...AA394 - 405396 - 407
119ARGARGSERSER(chain 'A' and (resid 19 or (resid 20 and (name...AA408 - 460410 - 462
21LYSLYSLEULEU(chain 'B' and (resid 19 through 25 or resid 27...BB19 - 2421 - 26
22LEULEULYSLYS(chain 'B' and (resid 19 through 25 or resid 27...BB27 - 2829 - 30
23ASNASNSERSER(chain 'B' and (resid 19 through 25 or resid 27...BB31 - 3333 - 35
24GLUGLULYSLYS(chain 'B' and (resid 19 through 25 or resid 27...BB36 - 4538 - 47
25SERSERLEULEU(chain 'B' and (resid 19 through 25 or resid 27...BB48 - 5450 - 56
26LYSLYSLYSLYS(chain 'B' and (resid 19 through 25 or resid 27...BB5860
27ASPASPASNASN(chain 'B' and (resid 19 through 25 or resid 27...BB60 - 6162 - 63
28PHEPHEGLUGLU(chain 'B' and (resid 19 through 25 or resid 27...BB64 - 7066 - 72
29SERSERALAALA(chain 'B' and (resid 19 through 25 or resid 27...BB73 - 11675 - 118
210LYSLYSVALVAL(chain 'B' and (resid 19 through 25 or resid 27...BB119 - 142121 - 144
211ILEILEGLNGLN(chain 'B' and (resid 19 through 25 or resid 27...BB145 - 199147 - 201
212THRTHRARGARG(chain 'B' and (resid 19 through 25 or resid 27...BB202 - 241204 - 243
213PROPROHISHIS(chain 'B' and (resid 19 through 25 or resid 27...BB243 - 268245 - 270
214GLYGLYTHRTHR(chain 'B' and (resid 19 through 25 or resid 27...BB271 - 289273 - 291
215GLYGLYASNASN(chain 'B' and (resid 19 through 25 or resid 27...BB292 - 319294 - 321
216THRTHRGLUGLU(chain 'B' and (resid 19 through 25 or resid 27...BB322 - 333324 - 335
217SERSERSERSER(chain 'B' and (resid 19 through 25 or resid 27...BB336 - 391338 - 393
218ASPASPLYSLYS(chain 'B' and (resid 19 through 25 or resid 27...BB394 - 405396 - 407
219ARGARGSERSER(chain 'B' and (resid 19 through 25 or resid 27...BB408 - 460410 - 462

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Components

#1: Protein Ankyrin repeat-containing protein


Mass: 52703.379 Da / Num. of mol.: 2
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: legA15, lpg2456 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZSR1
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris pH 8.5, 20% Glycerol, 2% acetonitrile and 22% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.5→47.94 Å / Num. obs: 67586 / % possible obs: 99.3 % / Redundancy: 2.2 % / Biso Wilson estimate: 39.01 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.02
Reflection shellResolution: 2.5→2.57 Å / Rmerge(I) obs: 0.454 / Num. unique obs: 4999

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→47.94 Å / SU ML: 0.2908 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.9522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2368 1741 5 %
Rwork0.1935 33083 -
obs0.1957 34824 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.31 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6790 0 53 254 7097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00477019
X-RAY DIFFRACTIONf_angle_d0.74529440
X-RAY DIFFRACTIONf_chiral_restr0.04221023
X-RAY DIFFRACTIONf_plane_restr0.00461250
X-RAY DIFFRACTIONf_dihedral_angle_d6.1323953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.29481450.2482752X-RAY DIFFRACTION100
2.57-2.660.28721450.22882742X-RAY DIFFRACTION99.97
2.66-2.750.28851430.23542736X-RAY DIFFRACTION99.93
2.75-2.860.26551440.22522731X-RAY DIFFRACTION99.93
2.86-2.990.29771450.23582756X-RAY DIFFRACTION100
2.99-3.150.25351450.22232741X-RAY DIFFRACTION99.93
3.15-3.350.25981440.2062737X-RAY DIFFRACTION99.93
3.35-3.610.24351440.19992744X-RAY DIFFRACTION99.93
3.61-3.970.26861460.18652780X-RAY DIFFRACTION100
3.97-4.540.19841450.16882748X-RAY DIFFRACTION99.9
4.54-5.720.21791470.16982787X-RAY DIFFRACTION99.83
5.72-47.940.1751480.16382829X-RAY DIFFRACTION99.67

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