7B6K | pdb_00007b6k

Crystal structure of MurE from E.coli in complex with Z57715447

• PDB DOI: https://doi.org/10.2210/pdb7B6K/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-12-07 Released: 2020-12-23 
• 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: 1.84 Å
• R-Value Free: 
  0.256 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.212 (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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 108.05 kDa 
• Atom Count: 7,715 
• Modeled Residue Count: 957 
• 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, B	496	Escherichia coli K-12	Mutation(s): 0  Gene Names: murE, b0085, JW0083 EC: 6.3.2.13
UniProt
Find proteins for P22188 (Escherichia coli (strain K12)) Explore P22188  Go to UniProtKB:  P22188

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SZ2 (Subject of Investigation/LOI)	E [auth A], G [auth B]	5-cyclohexyl-3-(pyridin-4-yl)-1,2,4-oxadiazole C13 H15 N3 O XXTHMVRJMJIERU-UHFFFAOYSA-N
CIT	F [auth A], I [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
DMS	C [auth A], H [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
IPA	D [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.256 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.212 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.693	α = 97.098
b = 58.903	β = 91.201
c = 74.011	γ = 104.598

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-23 
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: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2020-12-30
  Changes: Database references, Structure summary
• Version 1.2: 2024-01-31
  Changes: Data collection, Database references, Derived calculations, Refinement description