6VR7

Structure of a pseudomurein peptide ligase type C from Methanothermus fervidus

• PDB DOI: https://doi.org/10.2210/pdb6VR7/pdb

• Classification: LIGASE
• Organism(s): Methanothermus fervidus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2020-02-06 Released: 2021-02-10 
• Deposition Author(s): Carbone, V., Schofield, L.R., Sutherland-Smith, A.J., Ronimus, R.S., Subedi, B.P.
• Funding Organization(s): Royal Society of New Zealand

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.279 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 

Literature

Archaeal pseudomurein and bacterial murein cell wall biosynthesis share a common evolutionary ancestry

Subedi, B.P., Martin, W.F., Carbone, V., Duin, E.C., Cronin, B., Sauter, J., Schofield, L.R., Sutherland-Smith, A.J., Ronimus, R.S.

(2021) FEMS Microbes 2

• DOI: https://doi.org/10.1093/femsmc/xtab012

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 55.01 kDa 
• Atom Count: 3,839 
• Modelled Residue Count: 485 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mur ligase middle domain protein	A	492	Methanothermus fervidus	Mutation(s): 0  Gene Names: Mfer_0336
UniProt
Find proteins for E3GXV7 (Methanothermus fervidus (strain ATCC 43054 / DSM 2088 / JCM 10308 / V24 S)) Explore E3GXV7  Go to UniProtKB:  E3GXV7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AAE (Subject of Investigation/LOI)	G [auth A]	ACETOACETIC ACID C4 H6 O3 WDJHALXBUFZDSR-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.279 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.802	α = 90
b = 97.802	β = 90
c = 138.351	γ = 90

Software Package:

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

Structure Validation

Currently 6VR7 does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Carbone, V., Schofield, L.R., Sutherland-Smith, A.J., Ronimus, R.S., Subedi, B.P.

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

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 2.0: 2021-07-28
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
• Version 2.1: 2021-09-29
  Changes: Database references
• Version 2.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description