5F3R | pdb_00005f3r

Structure of oxidized UDP-galactopyranose mutase from Mycobacterium smegmatis in complex with magnesium ion

• PDB DOI: https://doi.org/10.2210/pdb5F3R/pdb

• Classification: ISOMERASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-03 Released: 2016-12-07 
• 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 Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Structural dynamics of UDP-galactopyranose mutase from Mycobacterium smegmatis

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

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: 48.91 kDa 
• Atom Count: 3,469 
• Modeled Residue Count: 391 
• Deposited Residue Count: 418 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-galactopyranose mutase	A	418	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: glf, MSMEG_6404, MSMEI_6236 EC: 5.4.99.9
UniProt
Find proteins for A0R629 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R629  Go to UniProtKB:  A0R629

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
DMS	D [auth A], E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.989	α = 90
b = 85.989	β = 90
c = 126.151	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-07 
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 General Medical Sciences (NIH/NIGMS)	United States	R01 GM100346

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description