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)

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
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wwPDB Validation 3D Report Full Report

Validation slider image for 9VP8

This is version 1.0 of the entry. See complete history.

Literature

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

Kim, J.H., Park, H.H., Kang, Y.J.

To be published.

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

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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... 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3T5P7Q7
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.