5XHP | pdb_00005xhp

Transferase with ligands

• PDB DOI: https://doi.org/10.2210/pdb5XHP/pdb

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


• Deposited: 2017-04-22 Released: 2018-05-02 
• Deposition Author(s): Park, J., Yoo, Y., Kim, Y.H., Cho, H.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.319 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.288 (Depositor), 0.290 (DCC) 
• R-Value Observed: 
  0.290 (Depositor) 

Literature

Crystal structure of L-arginine and UDP bounded glycosyltransfease

Park, J., Yoo, Y., 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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 80.5 kDa 
• Atom Count: 4,960 
• Modeled Residue Count: 606 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cytoplasmic protein	A [auth F], B [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	E [auth F], H [auth E]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
ARG	C [auth F], F [auth E]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O
MN	D [auth F], G [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.319 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.288 (Depositor), 0.290 (DCC) 
• R-Value Observed: 0.290 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.116	α = 90
b = 50.116	β = 90
c = 201.704	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: 2018-05-02 
Deposition Author(s): Park, J., Yoo, Y., Kim, Y.H., Cho, H.S.

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references, Derived calculations