7B6G | pdb_00007b6g

Crystal structure of MurE from E.coli in complex with Z1675346324

• PDB DOI: https://doi.org/10.2210/pdb7B6G/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-12-07 Released: 2021-01-13 
• Deposition Author(s): Koekemoer, L., Steindel, M., Fairhead, M., Talon, R., Douangamath, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Krojer, T., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

Crystal structure of MurE from E.coli

Koekemoer, L., Steindel, M., Fairhead, M., Talon, R., Douangamath, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Krojer, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 107.35 kDa 
• Atom Count: 7,649 
• Modelled Residue Count: 960 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase	A [auth AAA], B [auth BBB]	496	Escherichia coli	Mutation(s): 0  Gene Names: murE, GHR40_01000, NCTC12650_04426 EC: 6.3.2.13

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NUJ (Subject of Investigation/LOI)	D [auth BBB]	trans-3-[(2,6-dimethylpyrimidin-4-yl)(methyl)amino]cyclobutan-1-ol C11 H17 N3 O SEZOHQAJJCEOMQ-MGCOHNPYSA-N
DMS	C [auth AAA], E [auth BBB]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.276	α = 97.234
b = 58.293	β = 91.447
c = 74.115	γ = 105.313

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Koekemoer, L., Steindel, M., Fairhead, M., Talon, R., Douangamath, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Krojer, T., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Derived calculations, Refinement description