7Y3P

Salmonella typhimurium YbiB protein

• PDB DOI: https://doi.org/10.2210/pdb7Y3P/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. 14028s Wu
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-06-12 Released: 2023-06-14 
• Deposition Author(s): Zhai, L., Li, B.Q., Jia, H.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.285 
• R-Value Work: 0.242 
• R-Value Observed: 0.244 

Literature

Salmonella typhimurium YbiB protein

Zhai, L., Li, B.Q., Jia, H.H.

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: gel filtration

Macromolecule Content

• Total Structure Weight: 35.7 kDa 
• Atom Count: 2,359 
• Modelled Residue Count: 311 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein YbiB	A	324	Salmonella enterica subsp. enterica serovar Typhimurium str. 14028s Wu	Mutation(s): 0  Gene Names:  ybiB, B8V99_18480, DLQ59_12755, G3324_001994, G3973_002950, G4A17_003772, G4B34_002982, G4I57_002962, G4L20_002745, G4P03_002002, G4Y39_002911, G4Y40_003028, G9334_003279, G9G61_001645, G9W50_001218
UniProt
Find proteins for Q8ZQN6 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZQN6  Go to UniProtKB:  Q8ZQN6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.285 
• R-Value Work: 0.242 
• R-Value Observed: 0.244 
• Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.77	α = 90
b = 69.77	β = 90
c = 140.082	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Zhai, L., Li, B.Q., Jia, H.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	No.31900124

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 1.1: 2023-08-09
  Changes: Source and taxonomy
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.3: 2024-06-26
  Changes: Derived calculations
• Version 1.4: 2024-07-03
  Changes: Database references, Structure summary