9YKF | pdb_00009ykf

Crystal Structure of E. coli D23N YajL

• PDB DOI: https://doi.org/10.2210/pdb9YKF/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-10-07 Released: 2025-10-22 
• 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: 0.98 Å
• R-Value Free: 
  0.114 (Depositor), 0.115 (DCC) 
• R-Value Work: 
  0.097 (Depositor), 0.098 (DCC) 
• R-Value Observed: 
  0.097 (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: 42.78 kDa 
• Atom Count: 4,221 
• Modeled Residue Count: 392 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein/nucleic acid deglycase 3	A, B	199	Escherichia coli	Mutation(s): 1  Gene Names: yajL, thiJ, b0424, JW5057 EC: 3.1.2 (PDB Primary Data), 3.5.1 (PDB Primary Data), 3.5.1.124 (PDB Primary Data)
UniProt
Find proteins for Q46948 (Escherichia coli (strain K12)) Explore Q46948  Go to UniProtKB:  Q46948

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], L [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	F [auth A], G [auth A], H [auth A], I [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	J [auth A], K [auth A], P [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free:  0.114 (Depositor), 0.115 (DCC) 
• R-Value Work:  0.097 (Depositor), 0.098 (DCC) 
• R-Value Observed: 0.097 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.723	α = 90
b = 78.335	β = 90
c = 99.614	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: 2025-10-22 
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: 2025-10-22
  Type: Initial release