4EEC

Crystal Structure of the glycopeptide antibiotic sulfotransferase StaL complexed with A3P and desulfo-A47934.

• PDB DOI: https://doi.org/10.2210/pdb4EEC/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Streptomyces toyocaensis
• Expression System: Escherichia coli BL21(DE3), Streptomyces toyocaensis
• Mutation(s): No 


• Deposited: 2012-03-28 Released: 2012-07-04 
• Deposition Author(s): Shi, R., Cygler, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.272 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Literature

Structural basis of sulfonation of the glycopeptide antibiotic scaffold by the sulfotransferase StaL

Shi, R., Munger, C., Kalan, L., Sulea, T., Wright, G.D., Cygler, M.

(2012) Proc Natl Acad Sci U S A 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 65.55 kDa 
• Atom Count: 3,899 
• Modelled Residue Count: 502 
• Deposited Residue Count: 579 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
StaL	A, B	286	Streptomyces toyocaensis	Mutation(s): 0  Gene Names: stal
UniProt
Find proteins for Q8KLM3 (Streptomyces toyocaensis) Explore Q8KLM3  Go to UniProtKB:  Q8KLM3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
desulfo-A47934	C	7	Streptomyces toyocaensis	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A3P	D [auth A]	ADENOSINE-3'-5'-DIPHOSPHATE C10 H15 N5 O10 P2 WHTCPDAXWFLDIH-KQYNXXCUSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
3MY	C	D-PEPTIDE LINKING	C9 H10 Cl N O3		TYR
OMY	C	L-PEPTIDE LINKING	C9 H10 Cl N O4		TYR

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000812	C	desulfo-A47934	Glycopeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.272 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.442	α = 90
b = 82.583	β = 90
c = 123.076	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-04 
Deposition Author(s): Shi, R., Cygler, M.

Revision History  

• Version 1.0: 2012-07-04
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Other
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 2.0: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Polymer sequence, Refinement description
• Version 2.1: 2023-12-06
  Changes: Data collection, Derived calculations