5DU2 | pdb_00005du2

Structural analysis of EspG2 glycosyltransferase

• PDB DOI: https://doi.org/10.2210/pdb5DU2/pdb

• Classification: TRANSFERASE
• Organism(s): Actinomadura verrucosospora
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-18 Released: 2015-10-14 
• Deposition Author(s): Michalska, K., Elshahawi, S.I., Bigelow, L., Babnigg, G., Thorson, J.S., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)
• 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: 2.70 Å
• R-Value Free: 
  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of EspG2 glycosyltransferase

Michalska, K., Elshahawi, S.I., Bigelow, L., Babnigg, G., Thorson, J.S., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.27 kDa 
• Atom Count: 5,576 
• Modeled Residue Count: 737 
• Deposited Residue Count: 838 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EspG2 glycosyltransferase	A, B	419	Actinomadura verrucosospora	Mutation(s): 0  Gene Names: espG2
UniProt
Find proteins for A0A0R4I999 (Actinomadura verrucosospora) Explore A0A0R4I999  Go to UniProtKB:  A0A0R4I999

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35DU2

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.331	α = 90
b = 178.381	β = 90
c = 189.598	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MR-Rosetta	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Michalska, K., Elshahawi, S.I., Bigelow, L., Babnigg, G., Thorson, J.S., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U01GM098248

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description