1J2Z | pdb_00001j2z

Crystal structure of UDP-N-acetylglucosamine acyltransferase

• PDB DOI: https://doi.org/10.2210/pdb1J2Z/pdb

• Classification: TRANSFERASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-01-15 Released: 2004-01-27 
• Deposition Author(s): Lee, B.I., Suh, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.264 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of UDP-N-acetylglucosamine acyltransferase from Helicobacter pylori

Lee, B.I., Suh, S.W.

(2003) Proteins 53: 772-774

• PubMed: 14579368 
• DOI: https://doi.org/10.1002/prot.10436
• Primary Citation Related Structures: 
  1J2Z

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Organizational Affiliation: 
• Laboratory of Structural Proteomics, School of Chemistry and Molecular Engineering, Seoul National University, Seoul, Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 30.55 kDa 
• Atom Count: 2,189 
• Modeled Residue Count: 259 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase	A	270	Helicobacter pylori	Mutation(s): 0  Gene Names: lpxA EC: 2.3.1.129
UniProt
Find proteins for O25927 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25927  Go to UniProtKB:  O25927

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SOG	B [auth A]	octyl 1-thio-beta-D-glucopyranoside C14 H28 O5 S CGVLVOOFCGWBCS-RGDJUOJXSA-N
TLA	E [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.264 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.686	α = 90
b = 90.686	β = 90
c = 148.203	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-01-27 
Deposition Author(s): Lee, B.I., Suh, S.W.

Revision History  

• Version 1.0: 2004-01-27
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary