7B6P | pdb_00007b6p

Crystal structure of E.coli MurE - C269S C340S C450S in complex with Ellman's reagent

• PDB DOI: https://doi.org/10.2210/pdb7B6P/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-12-08 Released: 2020-12-23 
• Deposition Author(s): Koekemoer, L., Steindel, M., Fairhead, M., 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: 1.68 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 

Starting Model: experimental

Literature

Crystal structure of MurE from E.coli

Koekemoer, L., Steindel, M., Fairhead, M., 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 and gel filtration (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 and gel filtration (software)

Macromolecule Content 

• Total Structure Weight: 108.07 kDa 
• Atom Count: 7,699 
• 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): 3  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
9JT (Subject of Investigation/LOI)	C [auth A], G [auth B]	N-phenyl-2-selanylbenzamide C13 H11 N O Se PVPUYGNPKBMXGO-UHFFFAOYSA-N
CIT	F [auth A], I [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
EDO	J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA	D [auth A], E [auth A], H [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.59	α = 96.72
b = 58.94	β = 91.48
c = 74.38	γ = 104.47

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., 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: 2023-04-12
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary