5TNV

Crystal Structure of a Xylose isomerase-like TIM barrel Protein from Mycobacterium smegmatis in Complex with Magnesium

• PDB DOI: https://doi.org/10.2210/pdb5TNV/pdb

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


• Deposited: 2016-10-14 Released: 2016-11-09 
• Deposition Author(s): Cook, W.J., Fedorov, A.A., Fedorov, E.V., Huang, H., Bonanno, J.B., Gerlt, J.A., Almo, S.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free: 0.137 
• R-Value Observed: 0.116 

Literature

Crystal Structure of a Xylose isomerase-like TIM barrel Protein from Mycobacterium smegmatis in Complex with Magnesium

Cook, W.J., Fedorov, A.A., Fedorov, E.V., Huang, H., Bonanno, J.B., Gerlt, J.A., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.27 kDa 
• Atom Count: 2,864 
• Modelled Residue Count: 306 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AP endonuclease, family protein 2	A	326	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_6790, MSMEI_6607
UniProt
Find proteins for A0R760 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R760  Go to UniProtKB:  A0R760

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free: 0.137 
• R-Value Observed: 0.116 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.869	α = 90
b = 82.869	β = 90
c = 125.218	γ = 120

Software Package:

Software Name	Purpose
SHELXL	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELXCD	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Cook, W.J., Fedorov, A.A., Fedorov, E.V., Huang, H., Bonanno, J.B., Gerlt, J.A., Almo, S.C.

---

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

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2017-01-18
  Changes: Database references, Structure summary
• Version 1.2: 2017-05-03
  Changes: Database references, Structure summary
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 1.5: 2024-03-06
  Changes: Data collection, Database references