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- PDB-9l6b: A ROS-Sensing Transcription Factor Promotes RpoS Accumulation to ... -

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Basic information

Entry
Database: PDB / ID: 9l6b
TitleA ROS-Sensing Transcription Factor Promotes RpoS Accumulation to Resist Oxidative Stress
Components
  • UPF0225 protein YchJ -A
  • UPF0225 protein YchJ -B
  • UPF0225 protein YchJ -C
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: 2.3 Å
AuthorsYuan, X.L. / Wang, W.W.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: A ROS-Sensing Transcription Factor Promotes RpoS Accumulation to Resist Oxidative Stress
Authors: Yuan, X.L. / Wang, W.W.
History
DepositionDec 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 29, 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 -A
B: UPF0225 protein YchJ -B
C: UPF0225 protein YchJ -C


Theoretical massNumber of molelcules
Total (without water)17,1233
Polymers17,1233
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-35 kcal/mol
Surface area8780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.937, 58.937, 124.367
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-116-

HOH

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Components

#1: Protein UPF0225 protein YchJ -A


Mass: 6634.627 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, STM14_2121 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F6B249
#2: Protein UPF0225 protein YchJ -B


Mass: 6847.577 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, STM14_2121 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F6B249
#3: Protein/peptide UPF0225 protein YchJ -C


Mass: 3641.189 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, STM14_2121 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F6B249
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 61 %
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→29.469 Å / Mean I/σ(I) obs: 17.8 / Num. unique obs: 10294 / Rpim(I) all: 0.019 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.47 Å / SU ML: 0.2408 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.7168
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2712 505 4.91 %
Rwork0.229 9789 -
obs0.2309 10294 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.65 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 0 0 81 1276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011225
X-RAY DIFFRACTIONf_angle_d1.08841650
X-RAY DIFFRACTIONf_chiral_restr0.0535164
X-RAY DIFFRACTIONf_plane_restr0.0091217
X-RAY DIFFRACTIONf_dihedral_angle_d17.4616449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.530.27791350.22922351X-RAY DIFFRACTION100
2.53-2.90.33921390.25872386X-RAY DIFFRACTION99.92
2.9-3.650.30431070.25552463X-RAY DIFFRACTION100
3.65-29.470.24291240.21182589X-RAY DIFFRACTION100

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