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- PDB-7w42: Crystal structure of Bacillus subtilis YjoB -

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Basic information

Entry
Database: PDB / ID: 7w42
TitleCrystal structure of Bacillus subtilis YjoB
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 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized ATPase YjoB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.619 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 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized ATPase YjoB
B: Uncharacterized ATPase YjoB


Theoretical massNumber of molelcules
Total (without water)97,9522
Polymers97,9522
Non-polymers00
Water4,432246
1
A: Uncharacterized ATPase YjoB
B: Uncharacterized ATPase YjoB

A: Uncharacterized ATPase YjoB
B: Uncharacterized ATPase YjoB

A: Uncharacterized ATPase YjoB
B: Uncharacterized ATPase YjoB


Theoretical massNumber of molelcules
Total (without water)293,8556
Polymers293,8556
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area39120 Å2
ΔGint-144 kcal/mol
Surface area98650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.600, 155.600, 303.081
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Uncharacterized ATPase YjoB


Mass: 48975.781 Da / Num. of mol.: 2
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 3.63 Å3/Da / Density % sol: 66.13 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 5% (v/v) PEG 400, 2 M ammonium, citrate/citric acid (pH 7.5), 10 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.619→50 Å / Num. obs: 42649 / % possible obs: 99.8 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 16.6
Reflection shellResolution: 2.62→2.72 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 4419

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Processing

Software
NameVersionClassification
PHENIXdev_3051refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 2.619→36.302 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 2244 5.26 %
Rwork0.1998 40401 -
obs0.2017 42645 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.03 Å2 / Biso mean: 49.2697 Å2 / Biso min: 19 Å2
Refinement stepCycle: final / Resolution: 2.619→36.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6488 0 0 246 6734
Biso mean---47.11 -
Num. residues----799
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6191-2.6760.32231340.2521248199
2.676-2.73820.38011460.26762486100
2.7382-2.80670.34291270.25752545100
2.8067-2.88250.29891180.23922509100
2.8825-2.96730.29711410.23332494100
2.9673-3.06310.29011440.23272522100
3.0631-3.17250.26121580.22932478100
3.1725-3.29940.28011380.22572519100
3.2994-3.44950.24051430.19342507100
3.4495-3.63120.20981480.18462514100
3.6312-3.85840.22611600.1792511100
3.8584-4.1560.21281220.17382546100
4.156-4.57350.19261190.16142552100
4.5735-5.23360.17211640.17232540100
5.2336-6.58730.231480.21382561100
6.5873-36.3020.23591340.2059263698

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