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- PDB-7w46: Crystal structure of Bacillus subtilis YjoB with ADP -

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Basic information

Entry
Database: PDB / ID: 7w46
TitleCrystal structure of Bacillus subtilis YjoB with ADP
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
ADENOSINE-5'-DIPHOSPHATE / Uncharacterized ATPase YjoB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3793
Polymers97,9522
Non-polymers4271
Water2,918162
1
A: Uncharacterized ATPase YjoB
B: Uncharacterized ATPase YjoB
hetero molecules

A: Uncharacterized ATPase YjoB
B: Uncharacterized ATPase YjoB
hetero molecules

A: Uncharacterized ATPase YjoB
B: Uncharacterized ATPase YjoB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,1369
Polymers293,8556
Non-polymers1,2823
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 area41050 Å2
ΔGint-167 kcal/mol
Surface area98270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.259, 156.259, 302.761
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: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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, 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: 2.7→50 Å / Num. obs: 39371 / % possible obs: 100 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 16.2
Reflection shellResolution: 2.7→2.81 Å / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4361

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Processing

Software
NameVersionClassification
PHENIXdev_3051refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W42

7w42


Resolution: 2.7→45.122 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 1940 4.94 %
Rwork0.1873 37355 -
obs0.1891 39295 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.5 Å2 / Biso mean: 49.7228 Å2 / Biso min: 19.3 Å2
Refinement stepCycle: final / Resolution: 2.7→45.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6480 0 27 162 6669
Biso mean--39.22 44.65 -
Num. residues----798
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.76750.33251480.28492625100
2.7675-2.84230.29621460.25592639100
2.8423-2.9260.28931360.21682610100
2.926-3.02040.26381370.22522652100
3.0204-3.12830.27121300.22842677100
3.1283-3.25350.27711310.21082630100
3.2535-3.40160.21831280.19222677100
3.4016-3.58080.21411260.19712660100
3.5808-3.80510.25381430.18752636100
3.8051-4.09870.21761320.17172712100
4.0987-4.51080.18621650.15192649100
4.5108-5.16270.16941390.15022674100
5.1627-6.50140.21861370.18872721100
6.5014-45.1220.19871420.1759279399

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