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- PDB-7w43: Crystal structure of Bacillus subtilis YjoB N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 7w43
TitleCrystal structure of Bacillus subtilis YjoB N-terminal domain
ComponentsUncharacterized ATPase YjoB
KeywordsHYDROLASE / AAA protein / chaperone
Function / homology
Function and homology information


Hydrolases / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
: / 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
Uncharacterized ATPase YjoB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDahal, P. / Kwon, E. / Kim, D.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Crystal structure and biochemical analysis suggest that YjoB ATPase is a putative substrate-specific molecular chaperone.
Authors: Kwon, E. / Dahal, P. / Kim, D.Y.
History
DepositionNov 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized ATPase YjoB
B: Uncharacterized ATPase YjoB
C: Uncharacterized ATPase YjoB
D: Uncharacterized ATPase YjoB
E: Uncharacterized ATPase YjoB
F: Uncharacterized ATPase YjoB
G: Uncharacterized ATPase YjoB
H: Uncharacterized ATPase YjoB
I: Uncharacterized ATPase YjoB
J: Uncharacterized ATPase YjoB
K: Uncharacterized ATPase YjoB
L: Uncharacterized ATPase YjoB


Theoretical massNumber of molelcules
Total (without water)228,02512
Polymers228,02512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54150 Å2
ΔGint-283 kcal/mol
Surface area77150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.333, 84.176, 180.222
Angle α, β, γ (deg.)90.000, 112.290, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Uncharacterized ATPase YjoB


Mass: 19002.100 Da / Num. of mol.: 12 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: yjoB, BSU12420 / Production host: Escherichia coli B (bacteria) / References: UniProt: O34703, Hydrolases

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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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 30% (w/v) isopropanol, 0.1 M Tris-HCl, 30% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 39002 / % possible obs: 96.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 11.4
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1935

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W42

7w42


Resolution: 3→49.36 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 1984 5.13 %
Rwork0.237 36701 -
obs0.2393 38685 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.09 Å2 / Biso mean: 83.5247 Å2 / Biso min: 40.83 Å2
Refinement stepCycle: final / Resolution: 3→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15526 0 0 0 15526
Num. residues----1853
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.070.41641370.37562573271096
3.08-3.160.35131340.34982607274197
3.16-3.250.37731460.33052592273897
3.25-3.360.37081400.29782608274896
3.36-3.480.34791360.26942527266393
3.48-3.610.30121390.25912608274797
3.62-3.780.25451440.24672621276597
3.78-3.980.29691430.23562626276997
3.98-4.230.28491410.22832602274397
4.23-4.550.26261360.19492569270594
4.55-5.010.22411450.20052668281398
5.01-5.740.27821450.21712695284099
5.74-7.220.27191420.2372667280997
7.22-49.360.2191560.19822738289497

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