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- PDB-9jrr: Crystal structure of YjgK from Salmonella Typhimurium -

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Basic information

Entry
Database: PDB / ID: 9jrr
TitleCrystal structure of YjgK from Salmonella Typhimurium
ComponentsDUF386 domain-containing protein
KeywordsSTRUCTURAL PROTEIN / YjgK / Salmonella enterica / zinc ion binding / DUF386 protein family / bacterial pathogenesis / structural homology / metal homeostasis
Function / homologyNanQ anomerase/TabA/YiaL family / NanQ anomerase/TabA/YiaL superfamily / YhcH/YjgK/YiaL / single-species biofilm formation / cytosol / DUF386 domain-containing protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsSeo, M.D. / Choi, S.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other governmentGRRCAjou2023-B03 Korea, Republic Of
CitationJournal: Proteins / Year: 2025
Title: Crystal Structure and Functional Characterization of YjgK From Salmonella Typhimurium.
Authors: Choi, S.Y. / Kim, E. / Yoon, H. / Kim, H.N. / Kim, J.H. / Seok, S.H. / Seo, M.D.
History
DepositionSep 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF386 domain-containing protein
B: DUF386 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7314
Polymers35,6002
Non-polymers1312
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-81 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.082, 86.896, 91.174
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein DUF386 domain-containing protein / Putative cytoplasmic protein / Toxin-antitoxin biofilm protein TabA / YhcH/YjgK/YiaL family protein


Mass: 17800.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: yjgK_2, AAB27_19150, AU613_09095, AVC05_00930, B1P38_04325, CE70_12930, CFF59_06540, CVR97_09725, DD95_15535, DPF41_00985, DPS76_02775, DRM14_08175, DU071_05470, E0935_03375, EER35_05400, F3R12_ ...Gene: yjgK_2, AAB27_19150, AU613_09095, AVC05_00930, B1P38_04325, CE70_12930, CFF59_06540, CVR97_09725, DD95_15535, DPF41_00985, DPS76_02775, DRM14_08175, DU071_05470, E0935_03375, EER35_05400, F3R12_06000, G0N82_09375, GB466_06445, SE14_04712
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6HP13
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15 M malic acid, 20% w/v polyethylene glycol (PEG) 3350, and pH 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.76→40.37 Å / Num. obs: 31986 / % possible obs: 96.93 % / Redundancy: 5.1 % / Biso Wilson estimate: 15.23 Å2 / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 18.96
Reflection shellResolution: 1.764→1.827 Å / Mean I/σ(I) obs: 6.35 / Num. unique obs: 2536 / CC1/2: 0.968 / CC star: 0.992

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
PHENIX0.9.8.92model building
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.76→40.37 Å / SU ML: 0.158 / Cross valid method: FREE R-VALUE / Phase error: 17.1427
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2021 1989 6.23 %
Rwork0.1567 29938 -
obs0.1594 31927 96.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.1 Å2
Refinement stepCycle: LAST / Resolution: 1.76→40.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 2 592 3019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672487
X-RAY DIFFRACTIONf_angle_d0.92893385
X-RAY DIFFRACTIONf_chiral_restr0.06379
X-RAY DIFFRACTIONf_plane_restr0.0072439
X-RAY DIFFRACTIONf_dihedral_angle_d6.3227330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.810.2241200.1611614X-RAY DIFFRACTION74.64
1.81-1.860.23421290.15712002X-RAY DIFFRACTION91.58
1.86-1.910.21291440.16152093X-RAY DIFFRACTION97.56
1.91-1.970.22881380.15472169X-RAY DIFFRACTION99.48
1.97-2.040.20471500.14932189X-RAY DIFFRACTION99.57
2.04-2.130.20851380.1492153X-RAY DIFFRACTION99.78
2.13-2.220.23211410.15272175X-RAY DIFFRACTION99.61
2.22-2.340.20721550.15692162X-RAY DIFFRACTION99.23
2.34-2.490.21261370.16482173X-RAY DIFFRACTION99.53
2.49-2.680.22431530.16922199X-RAY DIFFRACTION99.75
2.68-2.950.20051370.17112229X-RAY DIFFRACTION99.29
2.95-3.370.2031450.15732187X-RAY DIFFRACTION98.86
3.37-4.250.17051510.14152224X-RAY DIFFRACTION98.59
4.25-40.370.1831510.15842369X-RAY DIFFRACTION99.41

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