4MNR | pdb_00004mnr

Crystal Structure of D,D-Transpeptidase Domain of Peptidoglycan Glycosyltransferase from Eggerthella lenta

• PDB DOI: https://doi.org/10.2210/pdb4MNR/pdb

• Classification: TRANSFERASE
• Organism(s): Eggerthella lenta DSM 2243
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-09-11 Released: 2013-09-25 
• Deposition Author(s): Kim, Y., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

Crystal Structure of D,D-Transpeptidase Domain of Peptidoglycan Glycosyltransferase from Eggerthella lenta

Kim, Y., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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)

Macromolecule Content 

• Total Structure Weight: 48.15 kDa 
• Atom Count: 3,467 
• Modeled Residue Count: 417 
• Deposited Residue Count: 457 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan glycosyltransferase	A	457	Eggerthella lenta DSM 2243	Mutation(s): 0  Gene Names: Elen_3042 EC: 2.4.1.129
UniProt
Find proteins for C8WPP1 (Eggerthella lenta (strain ATCC 25559 / DSM 2243 / CCUG 17323 / JCM 9979 / KCTC 3265 / NCTC 11813 / VPI 0255 / 1899 B)) Explore C8WPP1  Go to UniProtKB:  C8WPP1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	C [auth A], D [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.06	α = 90
b = 69.159	β = 90
c = 119.975	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
DM	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Kim, Y., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary