6D99 | pdb_00006d99

Crystal structure of Corynebacterium diphtheriae UDP-galactopyranose mutase in complex with UDP-GalNAc (open, oxidized)

• PDB DOI: https://doi.org/10.2210/pdb6D99/pdb

• Classification: ISOMERASE
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-04-28 Released: 2019-05-15 
• Deposition Author(s): Wangkanont, K., Kiessling, L.L., Forest, K.T.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Substrate recognition by FAD in UDP-galactopyranose mutase

Wangkanont, K., Forest, K.T., Kiessling, L.L.

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.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 47.45 kDa 
• Atom Count: 3,576 
• Modeled Residue Count: 386 
• Deposited Residue Count: 393 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-galactopyranose mutase	A	393	Corynebacterium diphtheriae	Mutation(s): 0  Gene Names: BU167_07490

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
UD2	D [auth A]	URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-NESSUJCYSA-N
IPA	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.01	α = 90
b = 98.01	β = 90
c = 127.28	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Wangkanont, K., Kiessling, L.L., Forest, K.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI063596
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI126592
National Science Foundation (NSF, United States)	United States	IOS1353674

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description