2PR1 | pdb_00002pr1

Crystal structure of the Bacillus subtilis N-acetyltransferase YlbP protein in complex with Coenzyme-A

• PDB DOI: https://doi.org/10.2210/pdb2PR1/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-05-03 Released: 2007-05-15 
• Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Vorontsov, I.I., Collart, F.R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.255 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Crystal structure of the Bacillus subtilis N-acetyltransferase YlbP protein in complex with Coenzyme-A.

Minasov, G., Shuvalova, L., Kiryukhina, O., Vorontsov, I.I., Collart, F.R., Joachimiak, A., Anderson, W.F.

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 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.2 kDa 
• Atom Count: 2,718 
• Modeled Residue Count: 301 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized N-acetyltransferase ylbP	A, B	163	Bacillus subtilis	Mutation(s): 0  Gene Names: ylbP, BSU15100 EC: 2.3.1
UniProt
Find proteins for O34468 (Bacillus subtilis (strain 168)) Explore O34468  Go to UniProtKB:  O34468

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	F [auth A], J [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
SO4	E [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CO	G [auth B], H [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C, D	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.255 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.572	α = 90
b = 148.572	β = 90
c = 102.29	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-15 
Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Vorontsov, I.I., Collart, F.R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-05-15
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-02-21
  Changes: Data collection, Database references, Structure summary