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- PDB-5xnb: Crystal structure of the IcmS-IcmW-DotL complex of the Legionella... -

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Basic information

Entry
Database: PDB / ID: 5xnb
TitleCrystal structure of the IcmS-IcmW-DotL complex of the Legionella type IVb secretion system
Components
  • DotL
  • IcmS protein
  • IcmW
KeywordsPROTEIN BINDING / Binding protein
Function / homology
Function and homology information


protein transport / membrane / 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
DotL / IcmS protein / IcmW / Type 4 adapter protein IcmW / Type 4 coupling protein DotL
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.594 Å
AuthorsXu, J. / Xu, D. / Zhu, Y.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370722 China
National Natural Science Foundation of China81530068 China
National Natural Science Foundation of China81322024 China
National Natural Science Foundation of China81561130162 China
CitationJournal: To Be Published
Title: Crystal Structure of The IcmS-IcmW Complex in the Legionella Type IVb Secretion System
Authors: Xu, J. / Xu, D. / Wan, M. / Yin, L. / Wang, X. / Wu, L. / Liu, Y. / Liu, X. / Zhou, Y. / Zhu, Y.
History
DepositionMay 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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

Downloads & links

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Assembly

Deposited unit
A: DotL
B: IcmS protein
C: IcmW
D: DotL
E: IcmS protein
F: IcmW
G: DotL
H: IcmS protein
I: IcmW
J: DotL
K: IcmS protein
L: IcmW
M: DotL
N: IcmS protein
O: IcmW
P: DotL
Q: IcmS protein
R: IcmW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,46123
Polymers256,41418
Non-polymers1,0465
Water5,116284
1
A: DotL
B: IcmS protein
C: IcmW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9454
Polymers42,7363
Non-polymers2091
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-65 kcal/mol
Surface area17440 Å2
MethodPISA
2
D: DotL
E: IcmS protein
F: IcmW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9454
Polymers42,7363
Non-polymers2091
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-64 kcal/mol
Surface area17850 Å2
MethodPISA
3
G: DotL
H: IcmS protein
I: IcmW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9454
Polymers42,7363
Non-polymers2091
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-62 kcal/mol
Surface area17390 Å2
MethodPISA
4
J: DotL
K: IcmS protein
L: IcmW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9454
Polymers42,7363
Non-polymers2091
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-64 kcal/mol
Surface area17470 Å2
MethodPISA
5
M: DotL
N: IcmS protein
O: IcmW


Theoretical massNumber of molelcules
Total (without water)42,7363
Polymers42,7363
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-65 kcal/mol
Surface area17520 Å2
MethodPISA
6
P: DotL
Q: IcmS protein
R: IcmW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9454
Polymers42,7363
Non-polymers2091
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-61 kcal/mol
Surface area17460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.862, 135.862, 125.664
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
DotL / IcmO protein


Mass: 12632.252 Da / Num. of mol.: 6 / Fragment: UNP residues 661-773
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: dotL, icmO / Plasmid: pGEX-6p-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O54524, UniProt: Q5ZYC6*PLUS
#2: Protein
IcmS protein / Protein of uncharacterised function (DUF3773) / Type IV secretion protein IcmS


Mass: 12753.623 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria)
Gene: icmS, A9P85_02475, ERS240541_02334, ERS240560_01730, ERS253249_00859, lpymg_00458, PtVF89_00590
Plasmid: pRSFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O54636
#3: Protein
IcmW / IcmW protein


Mass: 17349.844 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: icmW / Plasmid: pRSFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q48800, UniProt: Q5ZS31*PLUS
#4: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG3350, 0.1 M Bis-Tris, pH 6.0, 0.2 M MgCl2 and 0.05 M KBr

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: CCD / Date: Mar 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.59→33.27 Å / Num. obs: 79957 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.839 % / Biso Wilson estimate: 43.98 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.123 / Χ2: 0.996 / Net I/σ(I): 11.55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.59-2.753.7410.7372.01127130.6620.8698
2.75-2.943.8860.4633.2122300.8210.537100
2.94-3.173.890.2795.21112980.9260.32399.9
3.17-3.483.8660.1549.02104280.9780.17999.9
3.48-3.883.840.08815.0494350.9910.10299.7
3.88-4.483.8390.06120.683040.9960.07199.8
4.48-5.473.8420.05522.5970610.9960.06499.9
5.47-7.693.8060.05522.1754450.9970.06499.8
7.69-33.273.8140.02937.1130430.9990.03498.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.594→33.27 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 29.13
RfactorNum. reflection% reflection
Rfree0.2821 4008 5.02 %
Rwork0.2227 --
obs0.2256 79888 99.47 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Bsol: 31.125 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 118.86 Å2 / Biso mean: 46.03 Å2 / Biso min: 11.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.0079 Å20 Å20 Å2
2--2.0079 Å2-0 Å2
3---5.3913 Å2
Refinement stepCycle: final / Resolution: 2.594→33.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17266 0 70 284 17620
Biso mean--53.44 33.66 -
Num. residues----2196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317607
X-RAY DIFFRACTIONf_angle_d0.71323781
X-RAY DIFFRACTIONf_chiral_restr0.0492722
X-RAY DIFFRACTIONf_plane_restr0.0033071
X-RAY DIFFRACTIONf_dihedral_angle_d16.6626760
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5942-2.62470.36531170.32792428254591
2.6247-2.65670.4311360.34626112747100
2.6567-2.69030.41691660.316125862752100
2.6903-2.72570.33541330.290126822815100
2.7257-2.7630.31021280.279726312759100
2.763-2.80250.36381350.271626452780100
2.8025-2.84430.29151450.261525952740100
2.8443-2.88870.28891200.242426742794100
2.8887-2.9360.34361350.256625912726100
2.936-2.98660.32851560.258426132769100
2.9866-3.04090.33471560.257326222778100
3.0409-3.09940.33451350.263426172752100
3.0994-3.16260.33161510.258126182769100
3.1626-3.23130.32951510.2526052756100
3.2313-3.30640.31881290.258426832812100
3.3064-3.3890.33011340.248625812715100
3.389-3.48050.29731360.235726692805100
3.4805-3.58280.30471320.219926342766100
3.5828-3.69830.26451370.20762611274899
3.6983-3.83030.25021340.199226122746100
3.8303-3.98340.26831400.20672620276099
3.9834-4.16440.2471270.20226182745100
4.1644-4.38350.24891480.193526512799100
4.3835-4.65750.24681240.185726252749100
4.6575-5.0160.23461430.190126492792100
5.016-5.51870.28631330.212126032736100
5.5187-6.31250.27631470.244326032750100
6.3125-7.93530.25891510.197626292780100
7.9353-33.27310.18231290.16182574270398

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