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- PDB-5x42: Structure of DotL(590-659)-DotN derived from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 5x42
TitleStructure of DotL(590-659)-DotN derived from Legionella pneumophila
Components
  • DotN
  • IcmJ (DotN)
  • IcmO (DotL)
KeywordsPROTEIN TRANSPORT / Type IV secretion system / Coupling protein complex / Effector translocation
Function / homology
Function and homology information


protein transport / endonuclease activity / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / TraD/TraG, TraM recognition site / TraM recognition site of TraD and TraG / : / HNH nucleases / HNH nuclease / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DotN / Type 4 apparatus protein DotN / Type 4 coupling protein DotL
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Legionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKwak, M.J. / Kim, J.D. / 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
DepositionFeb 9, 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 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: DotN
B: IcmO (DotL)
C: IcmJ (DotN)
D: IcmO (DotL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0536
Polymers61,9224
Non-polymers1312
Water7,404411
1
A: DotN
B: IcmO (DotL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9533
Polymers29,8882
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-27 kcal/mol
Surface area13520 Å2
MethodPISA
2
C: IcmJ (DotN)
D: IcmO (DotL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1003
Polymers32,0342
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-27 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.683, 72.220, 170.435
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DotN / IcmJ protein / Type IV secretion protein IcmJ / Uncharacterised protein


Mass: 22173.303 Da / Num. of mol.: 1 / Fragment: UNP residues 7-201 / Mutation: E35A, R60A, S207A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria)
Gene: dotN, icmJ, ERS240541_02347, ERS253249_00846, PtVF89_00655
Production host: Escherichia coli (E. coli) / References: UniProt: O54599, UniProt: Q5ZYB7*PLUS
#2: Protein IcmO (DotL)


Mass: 7714.727 Da / Num. of mol.: 2 / Fragment: UNP residues 590-659
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
#3: Protein IcmJ (DotN)


Mass: 24319.541 Da / Num. of mol.: 1 / Fragment: UNP residues 2-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: icmJ, lpg0455 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZYB7
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.64 Å3/Da / Density % sol: 53.35 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 100mM sodium malonate (pH 4.0), 10%(v/v) PEG3350, 20%(v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.2828 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2828 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 104008 / % possible obs: 97 % / Redundancy: 8.8 % / Biso Wilson estimate: 26.31 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Χ2: 2.161 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.833.40.2720.4160.1490.3130.64491.2
1.83-1.863.70.2660.4880.1370.3030.67391.2
1.86-1.94.10.260.6090.1270.2920.73292
1.9-1.944.70.2590.7050.1190.2880.80194
1.94-1.985.20.2470.830.1050.270.89296.4
1.98-2.036.10.2390.90.0950.2591.01496.2
2.03-2.086.70.220.9440.0820.2361.0896.7
2.08-2.137.40.1930.9720.0690.2051.18497.7
2.13-2.28.20.1710.9820.0580.1811.28397.8
2.2-2.278.80.1510.9890.050.1591.32898.4
2.27-2.359.40.1350.9910.0430.1421.4398.1
2.35-2.449.90.1190.9930.0370.1251.50798.5
2.44-2.5510.50.1050.9970.0320.111.66298.5
2.55-2.6910.90.0960.9960.0290.1011.93598.7
2.69-2.8611.40.0930.9960.0280.0972.64699.1
2.86-3.0811.50.0880.9970.0260.0923.23198.7
3.08-3.3912.10.0750.9980.0220.0793.51599.3
3.39-3.8812.60.0560.9980.0160.0592.9999.4
3.88-4.8813.10.0460.9990.0130.0482.78899.5
4.88-5012.70.0480.9980.0140.053.78598.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→48.58 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.72 / Phase error: 28.18
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2598 3099 2.98 %
Rwork0.2107 --
obs0.2121 104008 92.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.34 Å2 / Biso mean: 37.9366 Å2 / Biso min: 15.93 Å2
Refinement stepCycle: final / Resolution: 1.8→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4112 0 2 411 4525
Biso mean--35.72 40.47 -
Num. residues----526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084184
X-RAY DIFFRACTIONf_angle_d0.845638
X-RAY DIFFRACTIONf_chiral_restr0.049624
X-RAY DIFFRACTIONf_plane_restr0.005731
X-RAY DIFFRACTIONf_dihedral_angle_d13.7852523
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82810.37311210.3553774389577
1.8281-1.85810.38511180.35123833395178
1.8581-1.89020.38971250.32983954407980
1.8902-1.92450.40631240.32544081420583
1.9245-1.96160.33591330.30214332446586
1.9616-2.00160.30221350.27254386452189
2.0016-2.04510.29541390.26374532467191
2.0451-2.09270.22531380.2574493463192
2.0927-2.1450.28881430.24194644478794
2.145-2.2030.34551480.24144713486195
2.203-2.26780.28261370.23474725486296
2.2678-2.3410.2721400.22734759489996
2.341-2.42470.2531470.22334796494397
2.4247-2.52180.26291470.21844822496997
2.5218-2.63660.33091470.23344790493798
2.6366-2.77550.2691500.21984874502498
2.7755-2.94940.27371490.2234872502198
2.9494-3.17710.29761500.22784886503699
3.1771-3.49680.30061520.20894869502199
3.4968-4.00250.24651530.178649615114100
4.0025-5.04190.16341510.146749095060100
5.0419-48.59820.20771520.17084904505699

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