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- PDB-9vxg: ROS-Sensing Transcription Factor YchJ Regulates the RssB-RpoS Pat... -

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Basic information

Entry
Database: PDB / ID: 9vxg
TitleROS-Sensing Transcription Factor YchJ Regulates the RssB-RpoS Pathway to Protect Salmonella Against Oxidative Attack by Macrophages
Components(UPF0225 protein YchJ) x 2
KeywordsDNA BINDING PROTEIN / DNA binding
Function / homologyUncharacterised protein family UPF0225 / : / YchJ, middle NTF2-like domain / SEC-C motif / SEC-C motif / NTF2-like domain superfamily / UPF0225 protein YchJ
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsYuan, X.L. / Wang, W.W.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: ROS-Sensing Transcription Factor YchJ Regulates the RssB-RpoS Pathway to Protect Salmonella Against Oxidative Attack by Macrophages
Authors: Wang, W.W. / Yuan, X.L.
History
DepositionJul 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0225 protein YchJ
B: UPF0225 protein YchJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6673
Polymers16,6022
Non-polymers651
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.937, 58.937, 124.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein UPF0225 protein YchJ


Mass: 14874.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
Gene: ychJ, STM1755 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8ZP43
#2: Protein/peptide UPF0225 protein YchJ


Mass: 1727.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
Gene: ychJ, STM1755 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8ZP43
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.25 Å3/Da / Density % sol: 62.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5 M Ammonium sulfate, 0.1 M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 2, 2023
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→53.26 Å / Num. obs: 10353 / % possible obs: 92.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 54.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.02 / Rrim(I) all: 0.132 / Net I/σ(I): 18
Reflection shellResolution: 2.303→2.43 Å / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 20 / Num. unique obs: 10294 / CC1/2: 0.999 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.15.1_3469: ???)refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.302→29.468 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 505 4.91 %
Rwork0.2316 --
obs0.2333 10294 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.302→29.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 1 20 1182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051202
X-RAY DIFFRACTIONf_angle_d0.7891620
X-RAY DIFFRACTIONf_dihedral_angle_d3.155712
X-RAY DIFFRACTIONf_chiral_restr0.051161
X-RAY DIFFRACTIONf_plane_restr0.005212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.302-2.53330.31621350.27622351X-RAY DIFFRACTION100
2.5333-2.89960.3191390.3062386X-RAY DIFFRACTION100
2.8996-3.65210.3351070.26852463X-RAY DIFFRACTION100
3.6521-29.4680.22251240.1962589X-RAY DIFFRACTION100

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