4A1I | pdb_00004a1i

ykud from B.subtilis

• PDB DOI: https://doi.org/10.2210/pdb4A1I/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: 1.76 Å
• R-Value Free: 
  0.218 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

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)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 144.13 kDa 
• Atom Count: 11,563 
• Modeled Residue Count: 1,316 
• Deposited Residue Count: 1,320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE L, D-TRANSPEPTIDASE YKUD	A, B, C, D, E, F, G, H	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	DA [auth E], IA [auth F], M [auth A], NA [auth G], Q [auth B], SA [auth H], V [auth C], Y [auth D]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4	AA [auth E], BA [auth E], CA [auth E], FA [auth F], GA [auth F], HA [auth F], I [auth A], J [auth A], K [auth A], KA [auth G], L [auth A], LA [auth G], MA [auth G], O [auth B], P [auth B], PA [auth H], QA [auth H], RA [auth H], S [auth C], T [auth C], U [auth C], X [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	EA [auth E], JA [auth F], N [auth A], OA [auth G], R [auth B], TA [auth H], W [auth C], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.218 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.45	α = 90
b = 91.85	β = 90.25
c = 123.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing

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: 2012-10-03
  Changes: Derived calculations
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description