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- PDB-6z0f: Crystal structure of the membrane pseudokinase YukC/EssB from Bac... -

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Basic information

Entry
Database: PDB / ID: 6z0f
TitleCrystal structure of the membrane pseudokinase YukC/EssB from Bacillus subtilis T7SS
ComponentsESX secretion system protein YukC
KeywordsMEMBRANE PROTEIN / Type VIIb secretion system / pseudokinase / Bacillus subtilis
Function / homologyType VII secretion system EssB / Type VII secretion system EssB, C-terminal / WXG100 protein secretion system (Wss), protein YukC / membrane => GO:0016020 / plasma membrane / ESX secretion system protein YukC
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.553 Å
AuthorsTassinari, M. / Bellinzoni, M. / Alzari, P.M. / Fronzes, R. / Gubellini, F.
Citation
Journal: Mbio / Year: 2022
Title: The Antibacterial Type VII Secretion System of Bacillus subtilis: Structure and Interactions of the Pseudokinase YukC/EssB.
Authors: Tassinari, M. / Doan, T. / Bellinzoni, M. / Chabalier, M. / Ben-Assaya, M. / Martinez, M. / Gaday, Q. / Alzari, P.M. / Cascales, E. / Fronzes, R. / Gubellini, F.
#1: Journal: Biorxiv / Year: 2020
Title: Central role and structure of the membrane pseudokinase YukC in the antibacterial Bacillus subtilis Type VIIb Secretion System
Authors: Tassinari, M. / Doan, T. / Bellinzoni, M. / Chabalier, M. / Ben-Assaya, M. / Martinez, M. / Gaday, Q. / Alzari, P.M. / Cascales, E. / Fronzes, R. / Gubellini, F.
History
DepositionMay 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESX secretion system protein YukC
B: ESX secretion system protein YukC


Theoretical massNumber of molelcules
Total (without water)97,8772
Polymers97,8772
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-23 kcal/mol
Surface area38320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.015, 83.41, 106.445
Angle α, β, γ (deg.)90, 108.16, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ESX secretion system protein YukC


Mass: 48938.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: yukC, BSU31890 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71070
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 15 %w/v PEG 2K, 0.1 M MgCl2, 50 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.553→29.42 Å / Num. obs: 26268 / % possible obs: 92.3 % / Redundancy: 6.1 % / CC1/2: 0.979 / Rmerge(I) obs: 0.227 / Rpim(I) all: 0.101 / Net I/σ(I): 4.7
Reflection shellResolution: 2.553→2.858 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.482 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1314 / CC1/2: 0.588 / Rpim(I) all: 0.579 / % possible all: 62.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YNQ, 4ANO

2ynq

4ano


Resolution: 2.553→29.42 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.885 / SU R Cruickshank DPI: 0.979 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.786 / SU Rfree Blow DPI: 0.356 / SU Rfree Cruickshank DPI: 0.373
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 1333 -RANDOM
Rwork0.2353 ---
obs0.2369 26268 65 %-
Displacement parametersBiso mean: 88.52 Å2
Baniso -1Baniso -2Baniso -3
1-9.8652 Å20 Å211.9594 Å2
2---6.5819 Å20 Å2
3----3.2833 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: LAST / Resolution: 2.553→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5827 0 0 8 5835
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0065957HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.748125HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2687SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1028HARMONIC5
X-RAY DIFFRACTIONt_it5957HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion811SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4415SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.19
X-RAY DIFFRACTIONt_other_torsion2.73
LS refinement shellResolution: 2.553→2.75 Å
RfactorNum. reflection% reflection
Rfree0.2785 31 -
Rwork0.2376 --
obs--6.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
112.302-2.2025.86363.3586-1.99866.78350.5709-0.62970.9692-0.6297-0.22930.98570.96920.9857-0.3417-0.13150.02520.2409-0.678-0.0764-0.7847114.711-11.93377.6504
20.13994.57657.11168.2638-4.23974.6492-0.080.4365-0.18950.43650.4369-0.7044-0.1895-0.7044-0.3569-0.18940.0080.0195-0.28240.1527-0.126479.5018-12.36871.3033
317.03074.10045.853802.09242.43440.4126-0.0250.2109-0.025-0.1025-0.020.2109-0.02-0.3102-0.493-0.13710.1794-0.6685-0.0095-0.332447.881-22.593855.5951
45.74832.3181-0.22184.59612.232713.34710.145-0.04881.0865-0.0488-0.2076-0.07551.0865-0.07550.0627-0.22920.10610.1162-0.84380.0211-0.430124.7487-32.353133.6264
56.9876-3.6401-5.832718.35172.819821.1575-0.5274-0.54151.8562-0.54150.4931-0.99141.8562-0.99140.03430.45870.25830.099-0.5024-0.0749-0.51528.3103-39.051316.3393
65.47141.60220.43517.7874-0.86556.9824-0.03830.2436-0.70810.2436-0.0923-0.2016-0.7081-0.20160.1306-0.63650.10590.1835-0.7124-0.0366-0.564694.95352.827794.4115
7-5.6764-2.85317.58046.1913-5.68316.5528-0.190.634-0.36760.634-0.1705-0.2979-0.3676-0.29790.3606-0.5629-0.12290.0467-0.36980.1605-0.272780.8084-17.761571.7185
810.40751.66155.062501.38992.63150.17050.1230.21130.123-0.4737-0.18370.2113-0.18370.3033-0.3017-0.10410.0261-0.3674-0.0111-0.023546.0589-20.784160.0348
911.6732-2.4463-3.69787.74312.541510.88050.77210.82690.1180.8269-0.4745-0.81160.118-0.8116-0.2976-0.2066-0.26820.2625-0.55860.0441-0.622912.1773-22.742959.7403
107.8224-5.5257-1.179812.40133.959919.45070.48241.2962-0.49051.2962-0.3163-1.153-0.4905-1.153-0.1661-0.1308-0.31370.47630.6218-0.2245-0.06890.9181-18.465274.0991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|204 }A3 - 204
2X-RAY DIFFRACTION2{ A|205 - A|211 }A205 - 211
3X-RAY DIFFRACTION3{ A|212 - A|259 }A212 - 259
4X-RAY DIFFRACTION4{ A|260 - A|338 }A260 - 338
5X-RAY DIFFRACTION5{ A|339 - A|386 }A339 - 386
6X-RAY DIFFRACTION6{ B|4 - B|204 }B4 - 204
7X-RAY DIFFRACTION7{ B|205 - B|211 }B205 - 211
8X-RAY DIFFRACTION8{ B|212 - B|259 }B212 - 259
9X-RAY DIFFRACTION9{ B|260 - B|338 }B260 - 338
10X-RAY DIFFRACTION10{ B|339 - B|377 }B339 - 377

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