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- PDB-5x90: Structure of DotL(656-783)-IcmS-IcmW-LvgA derived from Legionella... -

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Basic information

Entry
Database: PDB / ID: 5x90
TitleStructure of DotL(656-783)-IcmS-IcmW-LvgA derived from Legionella pneumophila
Components
  • (Hypothetical virulence ...) x 2
  • (IcmO (DotL)) x 2
  • (IcmW) x 2
  • IcmS
KeywordsPROTEIN TRANSPORT / Type IV secretion system / Coupling protein complex / Effector translocation
Function / homology
Function and homology information


protein transport / plasma membrane / cytoplasm
Similarity search - Function
Type IVb secretion, IcmS, effector-recruitment / : / Type IVb secretion, IcmS, effector-recruitment / TraD/TraG, TraM recognition site / TraM recognition site of TraD and TraG / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Type 4 adapter protein IcmW / Type 4 adapter protein LvgA / Type 4 coupling protein DotL / Type 4 adapter protein IcmS
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKim, H. / Kwak, M.J. / Kim, J.D. / Kim, Y.G. / Oh, B.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of Korea (NRF)2008-0061987 Korea, Republic Of
CitationJournal: Nat Microbiol / Year: 2017
Title: Architecture of the type IV coupling protein complex of Legionella pneumophila
Authors: Kwak, M.J. / Kim, J.D. / Kim, H. / Kim, C. / Bowman, J.W. / Kim, S. / Joo, K. / Lee, J. / Jin, K.S. / Kim, Y.G. / Lee, N.K. / Jung, J.U. / Oh, B.H.
History
DepositionMar 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: IcmS
F: IcmW
G: IcmO (DotL)
H: Hypothetical virulence protein
A: IcmS
B: IcmW
C: IcmO (DotL)
D: Hypothetical virulence protein


Theoretical massNumber of molelcules
Total (without water)122,2798
Polymers122,2798
Non-polymers00
Water00
1
E: IcmS
F: IcmW
G: IcmO (DotL)
H: Hypothetical virulence protein


Theoretical massNumber of molelcules
Total (without water)61,2844
Polymers61,2844
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12590 Å2
ΔGint-101 kcal/mol
Surface area23340 Å2
MethodPISA
2
A: IcmS
B: IcmW
C: IcmO (DotL)
D: Hypothetical virulence protein


Theoretical massNumber of molelcules
Total (without water)60,9954
Polymers60,9954
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11850 Å2
ΔGint-97 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.325, 152.325, 74.475
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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Protein , 5 types, 6 molecules EAFGBC

#1: Protein IcmS


Mass: 12682.545 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: icmS, lpg0442 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZYD0
#2: Protein IcmW


Mass: 17089.535 Da / Num. of mol.: 1 / Fragment: UNP residues 2-150
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: icmW, lpg2688 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZS31
#3: Protein IcmO (DotL)


Mass: 11949.626 Da / Num. of mol.: 1 / Fragment: UNP residues 672-779
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: icmO, lpg0446 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZYC6
#5: Protein IcmW


Mass: 16974.447 Da / Num. of mol.: 1 / Fragment: UNP residues 2-149
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: icmW, lpg2688 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZS31
#6: Protein IcmO (DotL)


Mass: 11878.548 Da / Num. of mol.: 1 / Fragment: UNP residues 672-778
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: icmO, lpg0446 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZYC6

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Hypothetical virulence ... , 2 types, 2 molecules HD

#4: Protein Hypothetical virulence protein


Mass: 19562.389 Da / Num. of mol.: 1 / Fragment: UNP residues 22-193
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: lpg0525 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZY48
#7: Protein Hypothetical virulence protein


Mass: 19459.268 Da / Num. of mol.: 1 / Fragment: UNP residues 25-195
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: lpg0525 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZY48

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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: 4.35 Å3/Da / Density % sol: 71.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM Bis-Tris (pH 5.5), 15%(v/v) PEG3350, 8mM spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 46584 / % possible obs: 97.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 64.94 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.041 / Rrim(I) all: 0.091 / Χ2: 1.784 / Net I/σ(I): 10.5 / Num. measured all: 194861
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.852.50.3721430.3790.2550.4520.40690.4
2.85-2.92.80.36122340.4430.2360.4340.41193.9
2.9-2.9630.3322500.5210.2080.3930.43894.8
2.96-3.023.10.30422060.6180.1850.3580.48495.2
3.02-3.083.20.27123250.7380.1630.3180.49996.6
3.08-3.153.40.25222580.7980.1460.2930.57397.2
3.15-3.233.50.22123710.8780.1260.2560.62298.3
3.23-3.323.90.19823350.910.1070.2260.84698.3
3.32-3.424.10.1722970.9450.090.1930.91298.5
3.42-3.534.20.15723660.9630.0810.1771.2898.7
3.53-3.654.10.13923170.9680.0730.1571.63198.6
3.65-3.84.50.12623790.980.0630.1411.92999.5
3.8-3.9750.10823410.9870.0510.122.09399.5
3.97-4.185.20.09123590.9910.0420.1012.487100
4.18-4.445.20.07923750.9930.0370.0872.71399.9
4.44-4.795.30.07123440.9940.0330.0782.71299.8
4.79-5.274.90.06823780.9940.0330.0762.75299.7
5.27-6.035.10.06823630.9940.0320.0752.66199.7
6.03-7.595.50.05823720.9970.0270.0642.44199.9
7.59-505.10.04423500.9970.0210.0492.35799.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X1E

5x1e


Resolution: 2.8→41.432 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2947 1655 3.55 %
Rwork0.2515 44929 -
obs0.2531 46584 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.64 Å2 / Biso mean: 64.3885 Å2 / Biso min: 20.88 Å2
Refinement stepCycle: final / Resolution: 2.8→41.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8058 0 0 0 8058
Num. residues----1068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068219
X-RAY DIFFRACTIONf_angle_d0.94311172
X-RAY DIFFRACTIONf_chiral_restr0.0511298
X-RAY DIFFRACTIONf_plane_restr0.0061433
X-RAY DIFFRACTIONf_dihedral_angle_d14.454930
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.88240.34651230.28263533365692
2.8824-2.97540.33161260.28163625375195
2.9754-3.08170.3351470.28783662380996
3.0817-3.20510.39521360.27843698383497
3.2051-3.35090.29021300.2633768389899
3.3509-3.52740.30981410.25353823396499
3.5274-3.74830.31441400.25193761390199
3.7483-4.03750.32361410.238138103951100
4.0375-4.44340.26361460.215337953941100
4.4434-5.08540.27111460.21838183964100
5.0854-6.40320.25541420.262838193961100
6.4032-41.43660.28621370.267538173954100

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