9YFS | pdb_00009yfs

Protiated E. coli YajL, 100K

• PDB DOI: https://doi.org/10.2210/pdb9YFS/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-09-26 Released: 2025-10-08 
• Deposition Author(s): Lin, J., Kovalevsky, A., Walker, A.R., Wilson, M.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.94 Å
• R-Value Free: 
  0.137 (Depositor), 0.139 (DCC) 
• R-Value Work: 
  0.121 (Depositor), 0.123 (DCC) 
• R-Value Observed: 
  0.121 (Depositor) 

Starting Model: experimental

Literature

Environmental contributions to proton sharing in protein low barrier hydrogen bonds

Lin, J., Gerlits, O., Kneller, D.W., Weiss, K.L., Coates, L., Hix, M.A., Effah, S.Y., Kovalevsky, A., Walker, A.R., Wilson, M.A.

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: homology

Macromolecule Content 

• Total Structure Weight: 42.28 kDa 
• Atom Count: 3,993 
• Modeled Residue Count: 390 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone YajL	A [auth B], B [auth A]	199	Escherichia coli	Mutation(s): 0  Gene Names: thiJ, ACU57_11870, AM266_04520, ERS085365_02411, ERS085416_01937, ERS139211_01908, ERS150873_01827, PU15_11320, PU38_04800, SK85_00449 EC: 3.5.1 (UniProt), 3.1.2 (UniProt), 3.5.1.124 (UniProt)
UniProt
Find proteins for Q46948 (Escherichia coli (strain K12)) Explore Q46948  Go to UniProtKB:  Q46948

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth B], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth B], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.94 Å
• R-Value Free:  0.137 (Depositor), 0.139 (DCC) 
• R-Value Work:  0.121 (Depositor), 0.123 (DCC) 
• R-Value Observed: 0.121 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.767	α = 90
b = 78.474	β = 90
c = 99.616	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Lin, J., Kovalevsky, A., Walker, A.R., Wilson, M.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM153337

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release