2HKL | pdb_00002hkl

Crystal structure of Enterococcus faecium L,D-transpeptidase C442S mutant

• PDB DOI: https://doi.org/10.2210/pdb2HKL/pdb

• Classification: TRANSFERASE
• Organism(s): Enterococcus faecium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-07-05 Released: 2007-05-22 
• Deposition Author(s): Delfosse, V., Hugonnet, J.-E., Magnet, S., Mainardi, J.-L., Arthur, M., Mayer, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Enterococcus faecium L,D-transpeptidase C442S mutant

Delfosse, V., Hugonnet, J.-E., Magnet, S., Mainardi, J.-L., Arthur, M., Mayer, C.

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 83.93 kDa 
• Atom Count: 6,210 
• Modeled Residue Count: 744 
• Deposited Residue Count: 750 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,D-TRANSPEPTIDASE	A, B, C	250	Enterococcus faecium	Mutation(s): 1  Gene Names: ldtfm
UniProt
Find proteins for Q3Y185 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)) Explore Q3Y185  Go to UniProtKB:  Q3Y185

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth B], F [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 211.14	α = 90
b = 132.66	β = 89.98
c = 70.12	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-22 
Deposition Author(s): Delfosse, V., Hugonnet, J.-E., Magnet, S., Mainardi, J.-L., Arthur, M., Mayer, C.

Revision History  

• Version 1.0: 2007-05-22
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description