8EYP

Joint X-ray/neutron structure of Salmonella typhimurium tryptophan synthase internal aldimine from microgravity-grown crystal

• PDB DOI: https://doi.org/10.2210/pdb8EYP/pdb

• Classification: LYASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhi, Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-28 Released: 2024-02-14 
• Deposition Author(s): Drago, V.N., Kovalevsky, A., Blakeley, M.P., Forsyth, V.T., Mueser, T.C.
• 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: 1.80 Å
• R-Value Free: 0.199 
• R-Value Work: 0.182 

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• Method: NEUTRON DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.288 
• R-Value Work: 0.224 

Literature

Neutron diffraction from a microgravity-grown crystal reveals the active site hydrogens of the internal aldimine form of tryptophan synthase

Drago, V.N., Devos, J.M., Blakeley, M.P., Forsyth, V.T., Parks, J.M., Kovalevsky, A., Mueser, T.C.

(2024) Cell Rep Phys Sci 5: 101827

• DOI: https://doi.org/10.1016/j.xcrp.2024.101827

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 71.87 kDa 
• Atom Count: 5,202 
• Modelled Residue Count: 650 
• Deposited Residue Count: 665 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase alpha chain	A	268	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 0  Gene Names: trpA, STM1727 EC: 4.2.1.20
UniProt
Find proteins for P00929 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P00929  Go to UniProtKB:  P00929

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase beta chain	B	397	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: trpB, STM1726 EC: 4.2.1.20
UniProt
Find proteins for P0A2K1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A2K1  Go to UniProtKB:  P0A2K1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.199 
• R-Value Work: 0.182 
• Space Group: C 1 2 1

• Method: NEUTRON DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.288 
• R-Value Work: 0.224 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.51	α = 90
b = 61.86	β = 94.74
c = 67.67	γ = 90

Software Package:

Software Name	Purpose
nCNS	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
LAUEGEN	data reduction
LSCALE	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-14 
Deposition Author(s): Drago, V.N., Kovalevsky, A., Blakeley, M.P., Forsyth, V.T., Mueser, T.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM137008-01A1

Revision History  

• Version 1.0: 2024-02-14
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references