6PMH

Structure of Epimerase Mth375 from the thermophilic pseudomurein-containing methanogen Methanothermobacter thermautotrophicus

• PDB DOI: https://doi.org/10.2210/pdb6PMH/pdb

• Classification: ISOMERASE
• Organism(s): Methanothermobacter thermautotrophicus str. Delta H
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-01 Released: 2020-07-08 
• Deposition Author(s): Carbone, V., Schofield, L.R., Sutherland-Smith, A.J., Ronimus, R.S.
• Funding Organization(s): Royal Society of New Zealand

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.178 
• R-Value Work: 0.147 
• R-Value Observed: 0.149 

Literature

Structure of a UDP-GALE 4-epimerase (Mth375) from the thermophilic pseudomurein-containing methanogen Methanothermobacter thermautotrophicus

Carbone, V., Schofield, L.R., Sutherland-Smith, A.J., Ronimus, R.S.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 43.07 kDa 
• Atom Count: 3,042 
• Modelled Residue Count: 330 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose 4-epimerase related protein	A	368	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0  Gene Names: MTH_375
UniProt
Find proteins for O26475 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26475  Go to UniProtKB:  O26475

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP (Subject of Investigation/LOI)	G [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
AMP (Subject of Investigation/LOI)	H [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.178 
• R-Value Work: 0.147 
• R-Value Observed: 0.149 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.815	α = 90
b = 113.815	β = 90
c = 239.873	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Carbone, V., Schofield, L.R., Sutherland-Smith, A.J., Ronimus, R.S.

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Funding Organization	Location	Grant Number
Royal Society of New Zealand	New Zealand	AGR1301

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-12-27
  Changes: Database references, Structure summary