5XYK | pdb_00005xyk

Structure of Transferase

• PDB DOI: https://doi.org/10.2210/pdb5XYK/pdb

• Classification: TRANSFERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-07-09 Released: 2018-07-11 
• Deposition Author(s): Park, J.B., Yoo, Y., Kim, J., Cho, H.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 
  0.286 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.261 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.262 (Depositor) 

Starting Model: experimental

Literature

Structure of Transferase

Park, J.B., Yoo, Y., Kim, J., Cho, H.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.25 kDa 
• Atom Count: 2,480 
• Modeled Residue Count: 303 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cytoplasmic protein	A [auth E]	348	Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74	Mutation(s): 0  Gene Names: STM474_2223
UniProt
Find proteins for E8XCX6 (Salmonella typhimurium (strain 4/74)) Explore E8XCX6  Go to UniProtKB:  E8XCX6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP (Subject of Investigation/LOI)	D [auth E]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
ARG (Subject of Investigation/LOI)	B [auth E]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O
MN (Subject of Investigation/LOI)	C [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free:  0.286 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.261 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.262 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.059	α = 90
b = 50.059	β = 90
c = 201.242	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-11 
Deposition Author(s): Park, J.B., Yoo, Y., Kim, J., Cho, H.S.

Revision History  

• Version 1.0: 2018-07-11
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description