4A1K

Ykud L,D-transpeptidase

• PDB DOI: https://doi.org/10.2210/pdb4A1K/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2011-09-15 Released: 2012-09-26 
• Deposition Author(s): Blaise, M., Fuglsang Midtgaard, S., Roi Midtgaard, S., Boesen, T., Thirup, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.212 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

Structures of Three New Crystal Forms of the Ykud L,D-Transpeptidase from B. Subtilis.

Blaise, M., Fuglsang Midtgaard, S., Roi Midtgaard, S., Boesen, T., Thirup, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.78 kDa 
• Atom Count: 1,482 
• Modelled Residue Count: 165 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE L, D-TRANSPEPTIDASE YKUD	A	165	Bacillus subtilis	Mutation(s): 2  EC: 2
UniProt
Find proteins for O34816 (Bacillus subtilis (strain 168)) Explore O34816  Go to UniProtKB:  O34816

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.212 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.9	α = 90
b = 59.9	β = 90
c = 117.75	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-26 
Deposition Author(s): Blaise, M., Fuglsang Midtgaard, S., Roi Midtgaard, S., Boesen, T., Thirup, S.

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Advisory, Data collection
• Version 1.2: 2023-12-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description