5EQD | pdb_00005eqd

Structure of oxidized UDP-galactopyranose mutase from Mycobacterium smegmatis in complex with UDP in opened and closed form

• PDB DOI: https://doi.org/10.2210/pdb5EQD/pdb

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


• Deposited: 2015-11-12 Released: 2016-11-23 
• 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: 1.83 Å
• R-Value Free: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (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.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.74 kDa 
• Atom Count: 7,387 
• Modeled Residue Count: 783 
• Deposited Residue Count: 800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-galactopyranose mutase	A, B	400	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], K [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
UDP	J [auth B]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
SO4	F [auth A], H [auth A], O [auth B], P [auth B], Q [auth B], R [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NO3	D [auth A], E [auth A], G [auth A], I [auth A], L [auth B], M [auth B], N [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
UDP	BindingDB:  5EQD	Kd: 3.50e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.188	α = 90
b = 132.184	β = 90
c = 135.654	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-11-23 
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: 2016-11-23
  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, Refinement description