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- PDB-8b3s: Structure of YjbA in complex with ClpC N-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 8b3s
TitleStructure of YjbA in complex with ClpC N-terminal Domain
Components
  • ATP-dependent Clp protease ATP-binding subunit ClpC / Negative regulator of tic competence clcC/mecB
  • UPF0736 protein B4122_0676,UPF0736 protein YjbA
KeywordsUNKNOWN FUNCTION / sporulation
Function / homology
Function and homology information


peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding
Similarity search - Function
UPF0736 / Protein of unknown function (DUF3603) / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain ...UPF0736 / Protein of unknown function (DUF3603) / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
UPF0736 protein J5227_16610 / ATP-dependent Clp protease ATP-binding subunit ClpC / Negative regulator of tic competence clcC/mecB / UPF0736 protein YjbA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsEvans, N.J. / Isaacson, R.L. / Camp, A.H. / Collins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Structure of YjbA in complex with ClpC N-terminal Domain
Authors: Evans, N.J. / Isaacson, R.L.
History
DepositionSep 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0736 protein B4122_0676,UPF0736 protein YjbA
Z: ATP-dependent Clp protease ATP-binding subunit ClpC / Negative regulator of tic competence clcC/mecB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8959
Polymers59,3182
Non-polymers5777
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Peak shifting was observed upon binding, isothermal titration calorimetry, Fitted data for YjbA ClpC interaction: dH = -19.5 +/- 0.6 kJ/mol; KD = 3.79 +/- 0.50 uM; N = 0.82 ...Evidence: gel filtration, Peak shifting was observed upon binding, isothermal titration calorimetry, Fitted data for YjbA ClpC interaction: dH = -19.5 +/- 0.6 kJ/mol; KD = 3.79 +/- 0.50 uM; N = 0.82 +/- 0.01 sites., assay for oligomerization, In an NMR Titration observing chemical shift perturbation peaks disappeared upon binding in a dose dependant manner.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.713, 69.713, 89.601
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein UPF0736 protein B4122_0676,UPF0736 protein YjbA


Mass: 42370.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: B4122_0676, B4417_4067, Bateq7PJ16_1268, DFO69_2911, J5227_16610, SC09_Contig19orf00439, yjbA, BSU11410
Strain: 168 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A085CA92, UniProt: O31597
#2: Protein ATP-dependent Clp protease ATP-binding subunit ClpC / Negative regulator of tic competence clcC/mecB


Mass: 16947.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_1475 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A164W157
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 41.96 % / Description: Rods
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 4% PEG 8000, 0.2 M Magnesium Chloride / Temp details: bench top incubator

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.09→29.9 Å / Num. obs: 28876 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 1 / Net I/σ(I): 9.8
Reflection shellResolution: 2.09→2.13 Å / Redundancy: 8.8 % / Num. unique obs: 1440 / CC1/2: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
SHELXDEphasing
ARP/wARPmodel building
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5hbn

5hbn


Resolution: 2.09→29.867 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 1470 5.11 %
Rwork0.1846 --
obs0.1871 28744 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→29.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 37 242 3393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023249
X-RAY DIFFRACTIONf_angle_d0.5144387
X-RAY DIFFRACTIONf_dihedral_angle_d4.2872686
X-RAY DIFFRACTIONf_chiral_restr0.037475
X-RAY DIFFRACTIONf_plane_restr0.004562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.16450.43091510.33852696X-RAY DIFFRACTION99
2.1645-2.25120.33331670.29632725X-RAY DIFFRACTION100
2.2512-2.35360.34221490.2762708X-RAY DIFFRACTION100
2.3536-2.47760.3061210.23962750X-RAY DIFFRACTION100
2.4776-2.63280.28511340.2152753X-RAY DIFFRACTION100
2.6328-2.83590.26851540.20562714X-RAY DIFFRACTION100
2.8359-3.1210.23691760.18342695X-RAY DIFFRACTION100
3.121-3.5720.21861200.16042755X-RAY DIFFRACTION100
3.572-4.49790.18031540.13072733X-RAY DIFFRACTION100
4.4979-29.8670.17411440.15282745X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.0773 Å / Origin y: -0.9208 Å / Origin z: 2.6425 Å
111213212223313233
T0.142 Å2-0.0195 Å2-0.0037 Å2-0.3377 Å2-0.0311 Å2--0.2353 Å2
L0.443 °2-0.182 °2-0.146 °2-1.2259 °20.1075 °2--1.7687 °2
S0.0061 Å °0.0972 Å °-0.0191 Å °-0.0484 Å °0.0626 Å °-0.0724 Å °-0.0329 Å °0.355 Å °-0.0505 Å °
Refinement TLS groupSelection details: all

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