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

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Basic information

Entry
Database: PDB / ID: 6exc
TitleCrystal structure of DotM cytoplasmic domain (residues 153-380),R314E/R315E
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: 2.16 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)


Theoretical massNumber of molelcules
Total (without water)52,9052
Polymers52,9052
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint2 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.430, 50.630, 55.440
Angle α, β, γ (deg.)102.52, 97.67, 95.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein IcmP (DotM)


Mass: 26452.426 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M potassium chloride 0.1 M HEPES pH 7.5 15% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→53.44 Å / Num. obs: 25233 / % possible obs: 97.1 % / Redundancy: 1.8 % / Rsym value: 0.133 / Net I/σ(I): 5.7
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.3 / CC1/2: 0.494 / Rsym value: 0.5 / % possible all: 95.3

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Processing

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

6exb


Resolution: 2.16→53.44 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.037 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26013 1217 4.8 %RANDOM
Rwork0.19643 ---
obs0.1995 24016 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.128 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å22.16 Å23.48 Å2
2---2.12 Å21.48 Å2
3---0.43 Å2
Refinement stepCycle: 1 / Resolution: 2.16→53.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3416 0 0 114 3530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193497
X-RAY DIFFRACTIONr_bond_other_d0.0020.023338
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.9654725
X-RAY DIFFRACTIONr_angle_other_deg1.08137714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5365422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02223.086162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.65815623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1531534
X-RAY DIFFRACTIONr_chiral_restr0.1030.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213832
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02738
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_it4.1575.3721700
X-RAY DIFFRACTIONr_mcbond_other4.1585.3711699
X-RAY DIFFRACTIONr_mcangle_it5.8568.032118
X-RAY DIFFRACTIONr_mcangle_other5.8558.0322119
X-RAY DIFFRACTIONr_scbond_it4.9626.0071797
X-RAY DIFFRACTIONr_scbond_other4.9646.0051795
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4918.7732607
X-RAY DIFFRACTIONr_long_range_B_refined9.66863.0724021
X-RAY DIFFRACTIONr_long_range_B_other9.66862.9853998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 86 -
Rwork0.313 1797 -
obs--95.92 %

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