4WH5 | pdb_00004wh5

Crystal structure of lincosamide antibiotic adenylyltransferase LnuA, lincomycin-bound

• PDB DOI: https://doi.org/10.2210/pdb4WH5/pdb
• Entry: 4WH5 supersedes: 4E8J

• Classification: transferase/antibiotic
• Organism(s): Staphylococcus haemolyticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-09-20 Released: 2014-11-05 
• Deposition Author(s): Stogios, P.J., Dong, A., Minasov, G., Evdokimova, E., Egorova, O., Kudritska, M., Yim, O., Courvalin, P., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF LINCOSAMIDE ANTIBIOTIC ADENYLYLTRANSFERASE LNUA, LINCOMYCIN BOUND

Stogios, P.J.

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: 39.57 kDa 
• Atom Count: 3,205 
• Modeled Residue Count: 316 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lincosamide resistance protein	A, B	162	Staphylococcus haemolyticus	Mutation(s): 0  Gene Names: linA
UniProt
Find proteins for P06107 (Staphylococcus haemolyticus) Explore P06107  Go to UniProtKB:  P06107

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3QB	F [auth A], I [auth B]	LINCOMYCIN C18 H34 N2 O6 S OJMMVQQUTAEWLP-KIDUDLJLSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], E [auth A], G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34wh5

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.447	α = 90
b = 63.444	β = 101.6
c = 60.808	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
StructureStudio	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-05 
Deposition Author(s): Stogios, P.J., Dong, A., Minasov, G., Evdokimova, E., Egorova, O., Kudritska, M., Yim, O., Courvalin, P., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• This entry supersedes: 4E8J

Revision History  

• Version 1.0: 2014-11-05
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.2: 2023-11-15
  Changes: Data collection, Database references
• Version 1.3: 2024-10-09
  Changes: Structure summary