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- PDB-5x1e: Structure of DotL(656-783)-IcmS-IcmW derived from Legionella pneu... -

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Basic information

Entry
Database: PDB / ID: 5x1e
TitleStructure of DotL(656-783)-IcmS-IcmW derived from Legionella pneumophila
Components
  • (IcmO (DotL)) x 2
  • (IcmS) x 2
  • IcmW
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 / IcmW / 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 coupling protein DotL / Type 4 adapter protein IcmS
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.999 Å
AuthorsKim, J.D. / Kwak, M.J. / 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
DepositionJan 25, 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 1.2Mar 20, 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: IcmS
B: IcmW
C: IcmO (DotL)
D: IcmS
E: IcmW
F: IcmO (DotL)


Theoretical massNumber of molelcules
Total (without water)80,9066
Polymers80,9066
Non-polymers00
Water2,270126
1
A: IcmS
B: IcmW
C: IcmO (DotL)


Theoretical massNumber of molelcules
Total (without water)40,4883
Polymers40,4883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-70 kcal/mol
Surface area16910 Å2
MethodPISA
2
D: IcmS
E: IcmW
F: IcmO (DotL)


Theoretical massNumber of molelcules
Total (without water)40,4173
Polymers40,4173
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-67 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.597, 75.803, 150.637
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 5 types, 6 molecules ABECDF

#1: Protein IcmS


Mass: 12149.954 Da / Num. of mol.: 1 / Fragment: UNP residues 5-114
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: 16974.447 Da / Num. of mol.: 2 / 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
#3: Protein IcmO (DotL)


Mass: 11363.930 Da / Num. of mol.: 1 / Fragment: UNP residues 672-773
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
#4: Protein IcmS


Mass: 12265.042 Da / Num. of mol.: 1 / Fragment: UNP residues 4-114
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
#5: Protein IcmO (DotL)


Mass: 11177.764 Da / Num. of mol.: 1 / Fragment: UNP residues 674-773
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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Non-polymers , 1 types, 126 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25%(v/v) PEG550 monoethylether, 100mM MES (pH 6.5), 10mM zinc sulfate and 5mM spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 97546 / % possible obs: 92 % / Redundancy: 5.4 % / Biso Wilson estimate: 16.37 Å2 / Rmerge(I) obs: 0.1 / Χ2: 4.875 / Net I/σ(I): 16.7 / Num. measured all: 262793
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.033.10.28922281.496185.5
2.03-2.073.40.25922941.461187.8
2.07-2.113.70.23323731.507190.1
2.11-2.1540.21723661.607190.8
2.15-2.23.80.19722611.658187.5
2.2-2.253.80.221180310.981168.5
2.25-2.313.60.19617403.533167
2.31-2.374.90.1624492.054193.3
2.37-2.445.20.15125062.232195.3
2.44-2.525.40.14825122.547195.3
2.52-2.615.70.1325472.762196.8
2.61-2.715.90.12525783.008197.6
2.71-2.846.10.11925653.628197.5
2.84-2.996.40.11125844.187198.2
2.99-3.176.60.10826355.363198.8
3.17-3.426.50.09926256.219198.6
3.42-3.765.70.09325787.056196
3.76-4.316.60.07625657.104195.7
4.31-5.437.40.06927147.422199.4
5.43-507.50.074285010.344198.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.999→36.756 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.72 / Phase error: 23.21 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.269 3529 4.08 %
Rwork0.2213 82965 -
obs0.2231 86494 85.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.84 Å2 / Biso mean: 23.0888 Å2 / Biso min: 4.43 Å2
Refinement stepCycle: final / Resolution: 1.999→36.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5371 0 0 126 5497
Biso mean---20.83 -
Num. residues----710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085458
X-RAY DIFFRACTIONf_angle_d0.9727407
X-RAY DIFFRACTIONf_chiral_restr0.051877
X-RAY DIFFRACTIONf_plane_restr0.006957
X-RAY DIFFRACTIONf_dihedral_angle_d13.1863320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9988-2.02620.27931020.26122281238360
2.0262-2.05510.28811220.25622895301774
2.0551-2.08580.31191300.25952975310577
2.0858-2.11840.30881280.24983091321979
2.1184-2.15310.3091340.25153083321780
2.1531-2.19020.27591340.24573082321680
2.1902-2.230.281830.27691934201750
2.23-2.27290.5121070.45772591269867
2.2729-2.31930.2543980.26412384248262
2.3193-2.36970.331450.21243409355488
2.3697-2.42480.24781430.20643496363989
2.4248-2.48550.28531520.21133504365691
2.4855-2.55270.20131540.2063539369391
2.5527-2.62780.29131540.20543639379394
2.6278-2.71250.28451490.2163654380394
2.7125-2.80950.25691620.21863698386094
2.8095-2.92190.271580.22283722388096
2.9219-3.05480.28311620.22993727388996
3.0548-3.21580.28841630.22753755391898
3.2158-3.41710.27481650.23073789395497
3.4171-3.68080.26531480.22163604375293
3.6808-4.05070.22451430.18243573371692
4.0507-4.63590.20191610.16443830399199
4.6359-5.8370.23571670.18613852401999
5.837-36.76210.2291650.18363858402399

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