4QUS | pdb_00004qus

1.28 Angstrom resolution crystal structure of predicted acyltransferase with acyl-CoA N-acyltransferase domain (ypeA) from Escherichia coli str. K-12 substr. MG1655

• PDB DOI: https://doi.org/10.2210/pdb4QUS/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli str. K-12 substr. MG1655
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-07-11 Released: 2014-07-23 
• Deposition Author(s): Halavaty, A.S., Filippova, E.V., Minasov, G., Flores, K.J., Dubrovska, I., Shuvalova, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 
  0.139 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.109 (Depositor), 0.111 (DCC) 
• R-Value Observed: 
  0.111 (Depositor) 

Starting Model: experimental

Literature

1.28 Angstrom resolution crystal structure of predicted acyltransferase with acyl-CoA N-acyltransferase domain (ypeA) from Escherichia coli str. K-12 substr. MG1655

Halavaty, A.S., Filippova, E.V., Minasov, G., Flores, K.J., Dubrovska, I., Shuvalova, L., 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: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.89 kDa 
• Atom Count: 3,101 
• Modeled Residue Count: 289 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyltransferase YpeA	A, B	149	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0  Gene Names: b2434, JW2427, ypeA EC: 2.3.1
UniProt
Find proteins for P76539 (Escherichia coli (strain K12)) Explore P76539  Go to UniProtKB:  P76539

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	E [auth B], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free:  0.139 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.109 (Depositor), 0.111 (DCC) 
• R-Value Observed: 0.111 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34qus

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.817	α = 90
b = 90.817	β = 90
c = 84.167	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-23 
Deposition Author(s): Halavaty, A.S., Filippova, E.V., Minasov, G., Flores, K.J., Dubrovska, I., Shuvalova, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description