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- PDB-6exb: Crystal structure of DotM cytoplasmic domain (residues 153-380), ... -

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Basic information

Entry
Database: PDB / ID: 6exb
TitleCrystal structure of DotM cytoplasmic domain (residues 153-380), native form
ComponentsIcmP (DotM)
KeywordsPROTEIN BINDING / Membrane protein / secretion system / type 4 secretion system / Legionella pneumophila / coupling complex
Function / homology: / DotM, C-terminal cytoplasmic domain / : / protein transport / plasma membrane / Type 4 apparatus protein DotM
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsMeir, A. / Waksman, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council321630 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Legionella DotM structure reveals a role in effector recruiting to the Type 4B secretion system.
Authors: Meir, A. / Chetrit, D. / Liu, L. / Roy, C.R. / Waksman, G.
History
DepositionNov 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: IcmP (DotM)
B: IcmP (DotM)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2014
Polymers53,0172
Non-polymers1842
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-12 kcal/mol
Surface area21840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.520, 118.520, 66.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein IcmP (DotM)


Mass: 26508.586 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)
Gene: icmP, lpg0445 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BLR / References: UniProt: Q5ZYC7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate pH 5.0 a 15% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.968 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.84→102.7 Å / Num. obs: 46854 / % possible obs: 99.85 % / Redundancy: 10.1 % / Rsym value: 0.098 / Net I/σ(I): 13.9
Reflection shellResolution: 1.84→1.89 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 1.2 / CC1/2: 0.513 / Rsym value: 0.029 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EXD

6exd


Resolution: 1.84→102.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.836 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.137 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25034 2246 4.9 %RANDOM
Rwork0.20156 ---
obs0.20405 43848 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.467 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.48 Å20 Å2
2--0.96 Å20 Å2
3----3.1 Å2
Refinement stepCycle: 1 / Resolution: 1.84→102.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3513 0 12 226 3751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193622
X-RAY DIFFRACTIONr_bond_other_d0.0020.023479
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.9714892
X-RAY DIFFRACTIONr_angle_other_deg1.1338033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42922.781169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8915652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.741539
X-RAY DIFFRACTIONr_chiral_restr0.1240.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213979
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02772
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1444.1331755
X-RAY DIFFRACTIONr_mcbond_other4.1384.1311754
X-RAY DIFFRACTIONr_mcangle_it5.5756.1792192
X-RAY DIFFRACTIONr_mcangle_other5.5756.1812193
X-RAY DIFFRACTIONr_scbond_it5.2574.8341867
X-RAY DIFFRACTIONr_scbond_other5.2564.8341867
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8966.9812701
X-RAY DIFFRACTIONr_long_range_B_refined9.89649.544320
X-RAY DIFFRACTIONr_long_range_B_other9.90249.4064281
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 161 -
Rwork0.367 3238 -
obs--99.94 %

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