4WY2 | pdb_00004wy2

Crystal structure of universal stress protein E from Proteus mirabilis in complex with UDP-3-O-[(3R)-3-hydroxytetradecanoyl]-N-acetyl-alpha-glucosamine

• PDB DOI: https://doi.org/10.2210/pdb4WY2/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Proteus mirabilis HI4320
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-15 Released: 2014-11-26 
• Deposition Author(s): Shumilin, I.A., Shabalin, I.G., Handing, K.B., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.202 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of universal stress protein E from Proteus mirabilis incomplex withUDP-3-O-[(3R)-3-hydroxytetradecanoyl]-N-acetyl-alpha-glucosamine

Shumilin, I.A., Minor, W.

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)

Macromolecule Content 

• Total Structure Weight: 37.42 kDa 
• Atom Count: 2,857 
• Modeled Residue Count: 308 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Universal stress protein E	A	319	Proteus mirabilis HI4320	Mutation(s): 0  Gene Names: uspE, PMI1202
UniProt
Find proteins for B4ETT2 (Proteus mirabilis (strain HI4320)) Explore B4ETT2  Go to UniProtKB:  B4ETT2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U20	B [auth A]	uridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-N-acetyl-D-glucosamine C31 H53 N3 O19 P2 TZSJGZGYQDNRRX-MPLCHSTDSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.202 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3MG6M

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.877	α = 90
b = 107.877	β = 90
c = 74.923	γ = 90

Software Package:

Software Name	Purpose
BLU-MAX	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Shumilin, I.A., Shabalin, I.G., Handing, K.B., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health	United States	--

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 1.1: 2015-01-14
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy
• Version 1.3: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.4: 2023-09-27
  Changes: Data collection, Refinement description