9VP8 | pdb_00009vp8

Crystal structure of YdjB from Salmonella enterica subsp. enterica serovar Typhi

• PDB DOI: https://doi.org/10.2210/pdb9VP8/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): Salmonella enterica subsp. enterica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-07-02 Released: 2025-10-22 
• Deposition Author(s): Kang, Y.J., Park, H.H., Kim, J.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.211 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of YdjB from Salmonella enterica subsp. enterica serovar Typhi

Kim, J.H., Park, H.H., Kang, Y.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 13.96 kDa 
• Atom Count: 1,091 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YdjB	A	129	Salmonella enterica subsp. enterica	Mutation(s): 0  Gene Names:  CQE41_24605, CQE41_26710, D4Z17_24465, D4Z17_25245, DO679_24685, DO679_25805, DTU87_24435, DTU87_24900, E0U76_23790, E0U76_24960, EHB73_24130, EHB73_25360, EUC09_23745, EUC09_25055, EZX96_24135, EZX96_25275, F3E63_24010, F3E63_25325, F9Q85_23760, F9X98_23685, F9X98_24595, FE718_22725, FE718_24365, FQS30_23565, FQS30_24460, G1G93_23595, G1G93_23875, G1H47_23580, G1H47_23880, G1H91_23595, G1H91_23880, G1I18_23580, G1I18_23860, G2927_23595, G2927_24200, G3A19_23495, G3A19_24225, G3A20_08050, G3A20_24365, GB022_24295, GB022_24500, GB054_22795, GB054_24050, GB132_23520, GB151_24070, GB151_25030, GB387_22430, GB387_24570, GB396_24800, GB396_25405, GB407_23420, GB407_24705, GB492_23470, GB492_24085, GB502_23000, GB574_23445, GB574_24220, GB577_23875, GB577_24545, GBS28_23930, GBS32_23475, GBS32_24220, GBW29_23760, GBW29_24500, GBX88_23450, GBX88_24260, GBX94_22210, GBX94_24300, GBY07_22650, GBY14_22545, GBY14_24165, GBY50_23665, GBY50_24595, GBZ99_23255, GBZ99_24525, GDM15_22805, GDM15_25520, GDM77_24145, GDM77_25870, MB64_25285, MB64_25625
UniProt
Find proteins for A0A3T5P7Q7 (Salmonella enterica I) Explore A0A3T5P7Q7  Go to UniProtKB:  A0A3T5P7Q7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.211 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.88	α = 90
b = 42.88	β = 90
c = 140.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Kang, Y.J., Park, H.H., Kim, J.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release