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- PDB-7bwk: Structure of DotL(656-783)-IcmS-IcmW-LvgA-VpdB(461-590) derived f... -

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Basic information

Entry
Database: PDB / ID: 7bwk
TitleStructure of DotL(656-783)-IcmS-IcmW-LvgA-VpdB(461-590) derived from Legionella pneumophila
Components
  • Hypothetical virulence protein
  • IcmO (DotL)
  • IcmS
  • IcmW
  • PNPLA domain-containing protein
KeywordsPROTEIN TRANSPORT / Dot/Icm Type 4B Secretion System / effector recognition / Type 4B coupling protein complex-effector complex / DotL-IcmSW-LvgA / VpdB
Function / homology
Function and homology information


lipid catabolic process / protein transport / hydrolase activity / plasma membrane / cytoplasm
Similarity search - Function
Type IVb secretion, IcmS, effector-recruitment / : / Type IVb secretion, IcmS, effector-recruitment / IcmW / : / TraD/TraG, TraM recognition site / TraM recognition site of TraD and TraG / Patatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. ...Type IVb secretion, IcmS, effector-recruitment / : / Type IVb secretion, IcmS, effector-recruitment / IcmW / : / TraD/TraG, TraM recognition site / TraM recognition site of TraD and TraG / Patatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. / : / Acyl transferase/acyl hydrolase/lysophospholipase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Type 4 adapter protein IcmW / PNPLA domain-containing protein / Type 4 adapter protein LvgA / Type 4 coupling protein DotL / Type 4 adapter protein IcmS
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsKim, H. / Kwak, M.J. / Oh, B.H.
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for effector protein recognition by the Dot/Icm Type IVB coupling protein complex.
Authors: Kim, H. / Kubori, T. / Yamazaki, K. / Kwak, M.J. / Park, S.Y. / Nagai, H. / Vogel, J.P. / Oh, B.H.
History
DepositionApr 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 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
A: IcmO (DotL)
B: IcmS
C: IcmW
D: Hypothetical virulence protein
E: PNPLA domain-containing protein
F: IcmO (DotL)
G: IcmS
H: IcmW
I: Hypothetical virulence protein
J: PNPLA domain-containing protein


Theoretical massNumber of molelcules
Total (without water)165,25010
Polymers165,25010
Non-polymers00
Water00
1
A: IcmO (DotL)
B: IcmS
C: IcmW
D: Hypothetical virulence protein
E: PNPLA domain-containing protein


Theoretical massNumber of molelcules
Total (without water)82,6255
Polymers82,6255
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15830 Å2
ΔGint-115 kcal/mol
Surface area29620 Å2
MethodPISA
2
F: IcmO (DotL)
G: IcmS
H: IcmW
I: Hypothetical virulence protein
J: PNPLA domain-containing protein


Theoretical massNumber of molelcules
Total (without water)82,6255
Polymers82,6255
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15700 Å2
ΔGint-110 kcal/mol
Surface area29870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.992, 188.992, 170.252
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein IcmO (DotL)


Mass: 14215.950 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: icmO, lpg0446 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZYC6
#2: 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 str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: icmS, lpg0442 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZYD0
#3: Protein IcmW


Mass: 17349.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: icmW, lpg2688 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZS31
#4: Protein Hypothetical virulence protein


Mass: 23533.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: lpg0525 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZY48
#5: Protein PNPLA domain-containing protein


Mass: 14842.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: lpg1227 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZW60

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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: 5.02 Å3/Da / Density % sol: 73.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM sodium cacodylate (pH 7.0) 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 25, 2018
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: 75746 / % possible obs: 99.5 % / Redundancy: 15.4 % / Biso Wilson estimate: 36.71 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.026 / Rrim(I) all: 0.109 / Χ2: 0.394 / Net I/σ(I): 4.3 / Num. measured all: 1165282
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.857.70.31137210.5570.1090.3310.26998.7
2.85-2.98.80.31137180.6720.1010.3280.28199.3
2.9-2.969.30.30337240.7290.0960.3190.29499
2.96-3.02100.29337200.8040.0890.3070.399.4
3.02-3.0810.70.27837180.8720.0810.290.31499.2
3.08-3.1511.60.26437450.9160.0740.2750.32899.4
3.15-3.2312.50.24537260.9490.0660.2540.34499.7
3.23-3.3213.40.21837430.9690.0560.2260.35999.6
3.32-3.4214.60.237650.980.050.2070.37799.7
3.42-3.5315.40.17537730.9890.0430.180.499.7
3.53-3.6516.40.15237400.9930.0360.1560.41199.6
3.65-3.816.50.13137700.9950.0310.1350.42499.6
3.8-3.97160.11737960.9960.0280.1210.43299.7
3.97-4.1817.90.137880.9970.0230.1030.44299.7
4.18-4.4420.80.08637950.9990.0180.0880.44799.9
4.44-4.7921.40.0838160.9990.0170.0820.44199.8
4.79-5.2721.10.08238280.9990.0170.0840.43299.7
5.27-6.0319.90.08638510.9990.0190.0880.42199.6
6.03-7.5918.80.07239070.9990.0160.0740.40999.6
7.59-5023.20.039410210.0080.040.40499.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X90

5x90


Resolution: 2.801→47.248 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 3840 5.07 %
Rwork0.199 71845 -
obs0.2014 75685 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.08 Å2 / Biso mean: 26.2788 Å2 / Biso min: 3.33 Å2
Refinement stepCycle: final / Resolution: 2.801→47.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10652 0 0 0 10652
Num. residues----1342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910858
X-RAY DIFFRACTIONf_angle_d1.01414676
X-RAY DIFFRACTIONf_chiral_restr0.0511638
X-RAY DIFFRACTIONf_plane_restr0.0051902
X-RAY DIFFRACTIONf_dihedral_angle_d17.3396643
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.801-2.83620.35211320.2923257098
2.8362-2.87350.33171200.2841263399
2.8735-2.91290.33161420.2809261499
2.9129-2.95450.32081400.2686262499
2.9545-2.99860.33551450.2601261899
2.9986-3.04540.29261510.2539261099
3.0454-3.09540.31061370.252263099
3.0954-3.14870.31631510.24532622100
3.1487-3.2060.28141280.23742637100
3.206-3.26760.29211340.23652648100
3.2676-3.33430.30261380.22652623100
3.3343-3.40680.28741390.22432654100
3.4068-3.4860.26121350.2122654100
3.486-3.57310.2481320.19832663100
3.5731-3.66970.22391650.18662601100
3.6697-3.77770.21461400.17622658100
3.7777-3.89950.23721410.17752658100
3.8995-4.03880.21571440.17432667100
4.0388-4.20050.19881420.16862644100
4.2005-4.39150.19951380.15372705100
4.3915-4.62280.18271450.15042662100
4.6228-4.91220.21721580.16292670100
4.9122-5.2910.20221650.16722690100
5.291-5.82260.19881310.17652708100
5.8226-6.66310.25271490.20372723100
6.6631-8.38720.22971400.17592778100
8.3872-47.2480.20641580.1729288199

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